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- PDB-1esu: S235A MUTANT OF TEM1 BETA-LACTAMASE -

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Basic information

Entry
Database: PDB / ID: 1esu
TitleS235A MUTANT OF TEM1 BETA-LACTAMASE
ComponentsBETA-LACTAMASE
KeywordsHYDROLASE / SERINE BETA-LACTAMASE / ANTIBIOTIC RESISTANCE
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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsFonze, E. / Charlier, P.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1995
Title: TEM1 beta-lactamase structure solved by molecular replacement and refined structure of the S235A mutant.
Authors: Fonze, E. / Charlier, P. / To'th, Y. / Vermeire, M. / Raquet, X. / Dubus, A. / Frere, J.M.
History
DepositionApr 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2000Provider: 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 1.4Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)29,0222
Polymers28,9261
Non-polymers961
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.931, 63.245, 88.746
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUE PRO 167 IS CIS PROLINE.
DetailsThe biological assembly is a monomer

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Components

#1: Protein BETA-LACTAMASE


Mass: 28925.994 Da / Num. of mol.: 1 / Mutation: S235A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P62593, beta-lactamase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.03 Å3/Da / Density % sol: 39.5 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Imidazole 0.1M pH7.0, ammonium sulfate 43 to 48%, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal grow
*PLUS
Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
20.1 Mimidazole1reservoir
310 mM1reservoirNaN3
443-48 %satammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: Oct 26, 1993
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.767→37.912 Å / Num. all: 17496 / Num. obs: 16584 / % possible obs: 72.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 12.4 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 35.6
Reflection shellResolution: 1.767→1.869 Å / Redundancy: 1.86 % / % possible all: 29.6
Reflection
*PLUS
Num. measured all: 48113

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Processing

Software
NameVersionClassification
X-GENdata scaling
X-GENdata reduction
X-PLORmodel building
X-PLOR3.1refinement
X-PLORphasing
RefinementResolution: 2→6 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rwork0.162 ---
obs0.162 12848 81 %-
all-13158 --
Rfree---RANDOM
Displacement parametersBiso mean: 15.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2026 0 5 137 2168
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_angle_deg3
X-RAY DIFFRACTIONx_dihedral_angle_d24
X-RAY DIFFRACTIONx_improper_angle_d1.4
X-RAY DIFFRACTIONx_mcbond_it1.361.5
X-RAY DIFFRACTIONx_mcangle_it1.862
X-RAY DIFFRACTIONx_scbond_it2.882
X-RAY DIFFRACTIONx_scangle_it4.332.5
LS refinement shellResolution: 2→2.07 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rwork0.22 909 -
obs--59.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PEP
X-RAY DIFFRACTION2PARAM.SO4TOP.SO4
X-RAY DIFFRACTION3TIP3P.PARAMETERTIP3P.TOPOLOGY
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 15.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg3
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rwork: 0.22

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