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- PDB-1fr1: REFINED CRYSTAL STRUCTURE OF BETA-LACTAMASE FROM CITROBACTER FREU... -

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Basic information

Entry
Database: PDB / ID: 1fr1
TitleREFINED CRYSTAL STRUCTURE OF BETA-LACTAMASE FROM CITROBACTER FREUNDII INDICATES A MECHANISM FOR BETA-LACTAM HYDROLYSIS
ComponentsBETA-LACTAMASE
KeywordsHYDROLASE / Antibiotic Resistance / Class C Beta-lactamase
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 speciesCitrobacter freundii (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsOefner, C. / D'Arcy, A. / Daly, J.J. / Winkler, F.K.
CitationJournal: Nature / Year: 1990
Title: Refined crystal structure of beta-lactamase from Citrobacter freundii indicates a mechanism for beta-lactam hydrolysis.
Authors: Oefner, C. / D'Arcy, A. / Daly, J.J. / Gubernator, K. / Charnas, R.L. / Heinze, I. / Hubschwerlen, C. / Winkler, F.K.
History
DepositionSep 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2001Provider: 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 / Item: _software.name
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-LACTAMASE
B: BETA-LACTAMASE


Theoretical massNumber of molelcules
Total (without water)79,5112
Polymers79,5112
Non-polymers00
Water8,143452
1
A: BETA-LACTAMASE


Theoretical massNumber of molelcules
Total (without water)39,7551
Polymers39,7551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BETA-LACTAMASE


Theoretical massNumber of molelcules
Total (without water)39,7551
Polymers39,7551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.07, 84.63, 89.77
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


Mass: 39755.250 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Citrobacter freundii (bacteria) / Strain: 1203 / References: UniProt: Q46041, beta-lactamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 452 / 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: 47.46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.6M sodium-potassium phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418
DetectorType: XENTRONICS / Detector: AREA DETECTOR / Date: Jan 1, 1989
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 51312 / Num. obs: 46181 / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.07

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Processing

Software
NameVersionClassification
CCP4PHASEmodel building
TNTrefinement
X-GENdata reduction
X-GENdata scaling
CCP4(PHASE)phasing
RefinementResolution: 2→6 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: tnt
RfactorNum. reflection% reflection
obs0.182 44634 87 %
Rfree-0 -
all-51312 -
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5605 0 0 452 6057
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.024
X-RAY DIFFRACTIONt_angle_deg2.5

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