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- PDB-1zg4: TEM1 beta lactamase -

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Basic information

Entry
Database: PDB / ID: 1zg4
TitleTEM1 beta lactamase
ComponentsBeta-lactamase TEM
KeywordsHYDROLASE
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 / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsStec, B. / Holtz, K.M. / Wojciechowski, C.L. / Kantrowitz, E.R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structure of the wild-type TEM-1 beta-lactamase at 1.55 A and the mutant enzyme Ser70Ala at 2.1 A suggest the mode of noncovalent catalysis for the mutant enzyme.
Authors: Stec, B. / Holtz, K.M. / Wojciechowski, C.L. / Kantrowitz, E.R.
History
DepositionApr 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase TEM


Theoretical massNumber of molelcules
Total (without water)31,5941
Polymers31,5941
Non-polymers00
Water3,495194
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.020, 62.840, 89.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-lactamase TEM / TEM-1 / Penicillinase


Mass: 31594.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla / Plasmid: PLASMID / Production host: Escherichia coli (E. coli) / References: UniProt: P62593, beta-lactamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.87 Å3/Da / Density % sol: 34.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: UCSD MARK II / Detector: AREA DETECTOR / Date: Nov 27, 1999
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. all: 32816 / Num. obs: 32816 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 14.1

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Processing

Software
NameClassification
SDMSdata collection
SDMSdata reduction
X-PLORmodel building
SHELXL-97refinement
SDMSdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BTL

1btl


Resolution: 1.55→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.24 -RANDOM
Rwork0.185 --
all0.186 32816 -
obs0.186 32816 -
Refinement stepCycle: LAST / Resolution: 1.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2030 0 0 194 2224
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_dihedral_angle_d22.8

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