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- PDB-1bza: BETA-LACTAMASE TOHO-1 FROM ESCHERICHIA COLI TUH12191 -

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Basic information

Entry
Database: PDB / ID: 1bza
TitleBETA-LACTAMASE TOHO-1 FROM ESCHERICHIA COLI TUH12191
ComponentsBETA-LACTAMASE
KeywordsHYDROLASE / BETA-LACTAMASE
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Beta-lactamase Toho-1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsIbuka, A. / Taguchi, A. / Ishiguro, M. / Fushinobu, S. / Ishii, Y. / Kamitori, S. / Okuyama, K. / Yamaguchi, K. / Konno, M. / Matsuzawa, H.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Crystal structure of the E166A mutant of extended-spectrum beta-lactamase Toho-1 at 1.8 A resolution.
Authors: Ibuka, A. / Taguchi, A. / Ishiguro, M. / Fushinobu, S. / Ishii, Y. / Kamitori, S. / Okuyama, K. / Yamaguchi, K. / Konno, M. / Matsuzawa, H.
History
DepositionOct 28, 1998Processing site: BNL
Revision 1.0Apr 27, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3963
Polymers28,2041
Non-polymers1922
Water2,432135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.309, 73.309, 99.374
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein BETA-LACTAMASE


Mass: 28203.936 Da / Num. of mol.: 1 / Mutation: E166A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: TUH12191 / Cellular location: PERIPLASM / Gene: BLA / Plasmid: PBSD / Cellular location (production host): CYTOPLASM / Gene (production host): BLA / Production host: Escherichia coli (E. coli) / Strain (production host): AS226 / References: UniProt: Q47066, beta-lactamase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE STRUCTURE DISPLAYS A TOPOLOGY SIMILAR TO THAT OF THE PC1 BETA-LACTAMASE OF S. AUREUS (HERZBERG, ...THE STRUCTURE DISPLAYS A TOPOLOGY SIMILAR TO THAT OF THE PC1 BETA-LACTAMASE OF S. AUREUS (HERZBERG, 1991, J. MOL. BIOL., 217:701-719, PROTEIN DATA BANK ENTRY 1BLM) AND TO THAT OF B. LICHENIFORMIS 749/C (KNOX ET AL., 1991, J. MOL. BIOL., 220:435-355, PROTEIN DATA BANK ENTRY 4BLM).

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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: 47 %
Description: DATA WERE COLLECTED USING THE WEISSENBERG METHOD
Crystal growpH: 4.5 / Details: pH 4.5
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 15 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.8 Mammonium sulfate1reservoir
2100 mMacetate1reservoir
315 mg/mlprotein1drop
45 mMTris-HCl1drop

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Nov 1, 1996 / Details: BENT PLANE MIRROR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→80 Å / Num. obs: 29252 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 23.8 Å2 / Rsym value: 0.07 / Net I/σ(I): 8.3
Reflection shellResolution: 1.8→1.86 Å / Rsym value: 0.38 / % possible all: 93.5
Reflection
*PLUS
Num. measured all: 172393 / Rmerge(I) obs: 0.072

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BLM

2blm


Resolution: 1.8→6 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.217 -10 %RANDOM
Rwork0.182 ---
obs0.182 27007 95.3 %-
Refinement stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2403 0 10 135 2548
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.357
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARM19X.PROTOPH19.PEP
X-RAY DIFFRACTION2PARM19.SOLTOPH19.PRO
X-RAY DIFFRACTION3PARHCSDX.PRO

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