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- PDB-1jz2: E. COLI (lacZ) BETA-GALACTOSIDASE-TRAPPED 2-F-GALACTOSYL-ENZYME I... -

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Basic information

Entry
Database: PDB / ID: 1jz2
TitleE. COLI (lacZ) BETA-GALACTOSIDASE-TRAPPED 2-F-GALACTOSYL-ENZYME INTERMEDIATE (ORTHORHOMBIC)
ComponentsBeta-Galactosidase
KeywordsHYDROLASE / TIM BARREL (ALPHA/BETA BARREL) / JELLY-ROLL BARREL / IMMUNOGLOBULIN / BETA SUPERSANDWICH
Function / homology
Function and homology information


alkali metal ion binding / lactose catabolic process / beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity / carbohydrate binding / magnesium ion binding / identical protein binding
Beta-galactosidase, domain 4 / Galactose-binding-like domain superfamily / Beta-Galactosidase/glucuronidase domain superfamily / Glycosyl hydrolases family 2, sugar binding domain / Glycoside hydrolase, family 2, beta-galactosidase / Glycoside hydrolase, family 2, active site / Glycoside hydrolase, family 2, conserved site / Glycoside hydrolase superfamily / Glycoside hydrolase-type carbohydrate-binding / Immunoglobulin-like fold ...Beta-galactosidase, domain 4 / Galactose-binding-like domain superfamily / Beta-Galactosidase/glucuronidase domain superfamily / Glycosyl hydrolases family 2, sugar binding domain / Glycoside hydrolase, family 2, beta-galactosidase / Glycoside hydrolase, family 2, active site / Glycoside hydrolase, family 2, conserved site / Glycoside hydrolase superfamily / Glycoside hydrolase-type carbohydrate-binding / Immunoglobulin-like fold / Galactose mutarotase-like domain superfamily / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2 / Glycoside hydrolase family 2, catalytic domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycoside hydrolase, family 2 / Beta galactosidase small chain/ domain 5 / Beta galactosidase small chain / Domain of unknown function (DUF4981) / Glycosyl hydrolases family 2, TIM barrel domain / Beta-galactosidase; Chain A, domain 5 - #10 / Beta-galactosidase; Chain A, domain 5 / Galactose-binding domain-like / Distorted Sandwich / Glycosidases / Jelly Rolls / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Beta-galactosidase
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJuers, D.H. / McCarter, J.D. / Mackenzie, L. / Withers, S.G. / Matthews, B.W.
Citation
Journal: Biochemistry / Year: 2001
Title: A Structural View of the Action of Escherichia Coli (Lacz) Beta-Galactosidase
Authors: Juers, D.H. / Heightman, T.D. / Vasella, A. / McCarter, J.D. / Mackenzie, L. / Withers, S.G. / Matthews, B.W.
#1: Journal: Protein Sci. / Year: 2000
Title: High Resolution Structure of Beta-Galactosidase in a New Crystal Form Reveals Multiple Metal-Binding Sites and Provides a Structural Basis for Alpha-Complementation
Authors: Juers, D.H. / Jacobson, R.H. / Wigley, D. / Zhang, X.J. / Huber, R.E. / Tronrud, D.E. / Matthews, B.W.
#2: Journal: Protein Sci. / Year: 1999
Title: Structural Comparisons of Tim Barrel Proteins Suggest Functional and Evolutionary Relationships between Beta-Galactosidase and Other Glycohydrolases
Authors: Juers, D.H. / Huber, R.E. / Matthews, B.W.
#3: Journal: Nature / Year: 1994
Title: Three-Dimensional Structure of Beta-Galactosidase from E. Coli
Authors: Jacobson, R.H. / Zhang, X.J. / Dubose, R.F. / Matthews, B.W.
#4: Journal: J.Mol.Biol. / Year: 1992
Title: Crystallization of beta-galactosidase from Escherichia coli
Authors: Jacobson, R.H. / Matthews, B.W.
Validation Report
SummaryFull reportAbout validation report
History
DepositionSep 13, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-Galactosidase
B: Beta-Galactosidase
C: Beta-Galactosidase
D: Beta-Galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)472,89499
Polymers465,8854
Non-polymers7,00995
Water53,2702957
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36250 Å2
ΔGint-43 kcal/mol
Surface area133610 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)151.500, 167.700, 201.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
Beta-Galactosidase / / E.C.3.2.1.23 / LACTASE / lacZ / beta-d-galactosidase


Mass: 116471.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: lacZ / Plasmid: pET15B / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00722, beta-galactosidase
#2: Sugar
ChemComp-2FG / 2-deoxy-2-fluoro-beta-D-galactopyranose


Type: D-saccharide, beta linking / Mass: 182.147 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H11FO5
IdentifierTypeProgram
b-D-Galp2fluoroIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 3048 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-NA / SODIUM ION / Sodium


Mass: 22.990 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Na
#5: Chemical...
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 69 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2957 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Bis-Tris, PEG 8000, MgCl2, NaCl, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP at 288K, pH 6.50
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion
Details: used macroseeding, Juers, D.H., (2000) Protein Sci., 9, 1685.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
2100 mMBis-Tris1droppH6.5
3200 mM1dropMgCl2
41 mMdithiothreitol1drop
55 mM1dropNaCl
610 %PEG80001reservoir
7100 mMbis-Tris1reservoirpH6.5
8200 mM1reservoirMgCl2
9100 mM1reservoirNaCl
1010 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→27.6 Å / Num. all: 273807 / Num. obs: 273807 / % possible obs: 92 % / Redundancy: 2.6 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10
Reflection shellHighest resolution: 2.1 Å / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.8 / % possible all: 60.5
Reflection
*PLUS
% possible obs: 91 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.8

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Processing

Software
NameVersionClassification
TNTrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DP0
Resolution: 2.1→27.6 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / Stereochemistry target values: TNT
RfactorNum. reflection% reflectionSelection details
Rfree0.27 3979 1.5 %RANDOM
Rwork0.167 ---
All-273807 --
Obs-273807 92 %-
Solvent computationSolvent model: BABINET PRINCIPLE / Bsol: 235 Å2 / ksol: 0.89 e/Å3
Displacement parametersBiso mean: 33.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å20 Å2
2--5.8 Å20 Å2
3----6.3 Å2
Refinement stepCycle: LAST / Resolution: 2.1→27.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32500 0 368 2957 35825
Refine LS restraints
Refinement-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.014337491.3
X-RAY DIFFRACTIONt_angle_deg2.75457111.7
X-RAY DIFFRACTIONt_dihedral_angle_d18.2192880
X-RAY DIFFRACTIONt_incorr_chiral_ct00
X-RAY DIFFRACTIONt_pseud_angle19.72481
X-RAY DIFFRACTIONt_trig_c_planes0.0159161.7
X-RAY DIFFRACTIONt_gen_planes0.01448727
X-RAY DIFFRACTIONt_it5.1335121.4
X-RAY DIFFRACTIONt_nbd0.055435
Refinement
*PLUS
Rfactor obs: 0.167 / Rfactor Rfree: 0.27 / Rfactor Rwork: 0.167
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refinement-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_angle_deg2.8
X-RAY DIFFRACTIONt_planar_d0.0151.7
X-RAY DIFFRACTIONt_plane_restr0.0147

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