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- PDB-1xx2: Refinement of P99 beta-lactamase from Enterobacter cloacae -

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Basic information

Entry
Database: PDB / ID: 1xx2
TitleRefinement of P99 beta-lactamase from Enterobacter cloacae
ComponentsBeta-lactamase
KeywordsHYDROLASE / CLASS C BETA-LACTAMASE / CEPHALOSPORINASE / PENICILLINASE / AMPC / ENTEROBACTER CLOACAE / ANTIBIOTIC RESISTANCE / SERINE HYDROLASE
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.88 Å
AuthorsKnox, J.R. / Sun, T.
Citation
Journal: Biochemistry / Year: 1994
Title: Crystallographic structure of a phosphonate derivative of the Enterobacter cloacae P99 cephalosporinase: mechanistic interpretation of a beta-lactamase transition-state analog.
Authors: Lobkovsky, E. / Billings, E.M. / Moews, P.C. / Rahil, J. / Pratt, R.F. / Knox, J.R.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Evolution of an enzyme activity: crystallographic structure at 2-A resolution of cephalosporinase from the ampC gene of Enterobacter cloacae P99 and comparison with a class A penicillinase.
Authors: Lobkovsky, E. / Moews, P.C. / Liu, H. / Zhao, H. / Frere, J.M. / Knox, J.R.
History
DepositionNov 3, 2004Deposition site: RCSB / Processing site: RCSB
SupersessionNov 23, 2004ID: 2BLT
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 12, 2014Group: Database references
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Revision 1.5Oct 13, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)78,5402
Polymers78,5402
Non-polymers00
Water7,927440
1
A: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)39,2701
Polymers39,2701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)39,2701
Polymers39,2701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.50, 83.47, 95.46
Angle α, β, γ (deg.)90.00, 90.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase / / Cephalosporinase


Mass: 39269.754 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Enterobacter cloacae (bacteria) / Strain: P99 / References: UniProt: P05364, beta-lactamase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 440 / 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: 2.34 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: PEG 8000, SODIUM CACODYLATE, MgCl2, NaN3, pH 6.5 - 8.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Feb 29, 1992 / Details: pinholes
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→100 Å / Num. obs: 51415 / % possible obs: 0.91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 39.5 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 40.5
Reflection shellResolution: 1.86→1.97 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.274 / Mean I/σ(I) obs: 2.7 / Num. unique all: 51415 / Rsym value: 0.274 / % possible all: 0.537

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Processing

Software
NameClassification
FRAMBOdata collection
X-GENdata reduction
PHASESphasing
CNSrefinement
X-GENdata scaling
RefinementMethod to determine structure: MIR
Starting model: pdb entry 2BLT

2blt
PDB Unreleased entry


Resolution: 1.88→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 3 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.214 2293 -RANDOM
Rwork0.175 ---
all-45635 --
obs-45635 77.4 %-
Displacement parametersBiso mean: 0.419 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.252 Å0.205 Å
Luzzati d res low-5 Å
Luzzati sigma a0.234 Å0.193 Å
Refinement stepCycle: LAST / Resolution: 1.88→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5502 0 0 440 5942
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0073
X-RAY DIFFRACTIONc_angle_deg1.44
X-RAY DIFFRACTIONc_dihedral_angle_deg23.9
X-RAY DIFFRACTIONc_improper_angle_deg0.91
X-RAY DIFFRACTIONc_mcbond_it1.325
X-RAY DIFFRACTIONc_scbond_it2.08
X-RAY DIFFRACTIONc_mcangle_it1.92
X-RAY DIFFRACTIONc_scangle_it2.94
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection obs% reflection obs (%)
1.88-20.28961980.2423380739
2-2.150.25613160.2131655767
2.15-2.360.25424120.2054771879
2.36-2.70.24344170.1916845986
2.7-3.380.22334690.1781929695
3.38-100.17124810.1438979899

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