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- PDB-1jz4: E. COLI (lacZ) BETA-GALACTOSIDASE-TRAPPED 2-DEOXY-GALACTOSYL-ENZY... -

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Basic information

Entry
Database: PDB / ID: 1jz4
TitleE. COLI (lacZ) BETA-GALACTOSIDASE-TRAPPED 2-DEOXY-GALACTOSYL-ENZYME INTERMEDIATE (Low Bis-Tris)
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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJuers, D.H. / 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 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jul 29, 2020Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _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 / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details
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)475,317136
Polymers466,0254
Non-polymers9,292132
Water70,4933913
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41720 Å2
ΔGint-48 kcal/mol
Surface area135540 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)149.500, 169.000, 200.800
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: 116506.266 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-2DG / 2-deoxy-alpha-D-galactopyranose


Type: D-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O5

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Non-polymers , 4 types, 4041 molecules

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


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-NA / SODIUM ION / Sodium


Mass: 22.990 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Na
#5: Chemical...
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 103 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3913 / 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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Aug 1, 1999 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 264902 / % possible obs: 90 % / Redundancy: 2.7 % / Biso Wilson estimate: 7.7 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 7.5
Reflection shellHighest resolution: 2.1 Å / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.3 / % possible all: 80.2
Reflection
*PLUS
% possible obs: 90 % / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.3

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Processing

Software
NameClassification
TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling
TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DP0
Resolution: 2.1→40 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / Stereochemistry target values: TNT
RfactorNum. reflection% reflectionSelection details
Rfree0.267 3827 1.5 %RANDOM
Rwork0.164 ---
All-264902 --
Obs-264902 90 %-
Solvent computationSolvent model: BABINET PRINCIPLE / Bsol: 175 Å2 / ksol: 0.74 e/Å3
Displacement parametersBiso mean: 20.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å20 Å2
2---0.4 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32500 0 477 3913 36890
Refine LS restraints
Refinement-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.016338171.3
X-RAY DIFFRACTIONt_angle_deg2.924457731.7
X-RAY DIFFRACTIONt_dihedral_angle_d17.9192880
X-RAY DIFFRACTIONt_incorr_chiral_ct00
X-RAY DIFFRACTIONt_pseud_angle1
X-RAY DIFFRACTIONt_trig_c_planes0.0199161.7
X-RAY DIFFRACTIONt_gen_planes0.01748727
X-RAY DIFFRACTIONt_it5.3335080
X-RAY DIFFRACTIONt_nbd0.164355
Refinement
*PLUS
Rfactor obs: 0.164 / Rfactor Rfree: 0.267 / Rfactor Rwork: 0.164
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refinement-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_angle_deg2.9
X-RAY DIFFRACTIONt_planar_d0.0191.7
X-RAY DIFFRACTIONt_plane_restr0.0177

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