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- PDB-1px4: E. COLI (LACZ) BETA-GALACTOSIDASE (G794A) WITH IPTG BOUND -

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Basic information

Entry
Database: PDB / ID: 1px4
TitleE. COLI (LACZ) BETA-GALACTOSIDASE (G794A) WITH IPTG BOUND
Componentsbeta-galactosidase
KeywordsHYDROLASE / loop conformation
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: 1.6 Å
AuthorsJuers, D.H. / Hakda, S. / Matthews, B.W. / Huber, R.E.
CitationJournal: Biochemistry / Year: 2003
Title: Structural Basis for the Altered Activity of Gly794 Variants of Escherichia coli Beta-Galactosidase
Authors: Juers, D.H. / Hakda, S. / Matthews, B.W. / Huber, R.E.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJul 2, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / 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_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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
Remark 600HETEROGEN EACH HETEROATOM HAS BEEN ASSIGNED A CHAIN ID AND RESIDUE NUMBER BASED ON AN EQUIVALENCY ...HETEROGEN EACH HETEROATOM HAS BEEN ASSIGNED A CHAIN ID AND RESIDUE NUMBER BASED ON AN EQUIVALENCY TO HETEROATOMS IN PDB ENTRY 1DP0 (NATIVE BETA-GALACTOSIDASE). THE NUMBERING IS AS FOLLOWS: 2001-2002 LIGAND IPT, ISOPROPYL-1-BETA-D-THIOGALACTOSIDE 3001-3999 IONS (MG++ AND NA+) 4001-7999 WATER MOLECULES THOSE WATER MOLECULES WITHOUT AN EQUIVALENT IN 1DP0 START AT 7500 8401-8799 DMS

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)475,136134
Polymers466,0814
Non-polymers9,054130
Water68,6913813
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area42220 Å2
ΔGint-88 kcal/mol
Surface area134650 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)149.490, 168.290, 200.44
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
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 / / Lactase


Mass: 116520.281 Da / Num. of mol.: 4 / Mutation: G794A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: lacZ / Plasmid: pET15b (novagen) / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00722, beta-galactosidase
#4: Sugar
ChemComp-IPT / 1-methylethyl 1-thio-beta-D-galactopyranoside / 1-(ISOPROPYLTHIO)-BETA-GALACTOPYRANSIDE / Isopropyl β-D-1-thiogalactopyranoside


Type: D-saccharide / Mass: 238.301 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H18O5S
IdentifierTypeProgram
isopropyl-1-b-D-thiogalactosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 3939 molecules

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


Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-NA / SODIUM ION / Sodium


Mass: 22.990 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Na
#5: Chemical...
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 94 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3813 / 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: 54.5 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, NACL, MGCL2, DTT, BIS-TRIS, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→31.5 Å / Num. all: 623765 / Num. obs: 623765 / % possible obs: 94.8 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 18.1
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 3 / % possible all: 90

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Processing

Software
NameClassification
SCALEPACKdata scaling
TNTrefinement
TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1dp0
Resolution: 1.6→31.5 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.239 9118 -Random
Rwork0.187 ---
Obs0.188 623765 94.8 %-
All-623765 --
Displacement parametersBiso mean: 0.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å20 Å2
2--1.5 Å20 Å2
3----1.1 Å2
Refinement stepCycle: LAST / Resolution: 1.6→31.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32504 0 468 3813 36785
Refine LS restraints
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.8
X-RAY DIFFRACTIONt_bond_d0.016
X-RAY DIFFRACTIONt_bfactor_corr5.2

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