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- PDB-1ewz: CRYSTAL STRUCTURE OF THE OXA-10 BETA-LACTAMASE FROM PSEUDOMONAS A... -

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Basic information

Entry
Database: PDB / ID: 1ewz
TitleCRYSTAL STRUCTURE OF THE OXA-10 BETA-LACTAMASE FROM PSEUDOMONAS AERUGINOSA
ComponentsBETA LACTAMASE OXA-10
KeywordsHYDROLASE / alpha/beta structure
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Beta-lactamase OXA-10
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsGolemi, D. / Maveyraud, L. / Vakulenko, S. / Tranier, S. / Ishiwata, A. / Kotra, L.P. / Samama, J.P. / Mobashery, S.
CitationJournal: J.Am.Chem.Soc. / Year: 2000
Title: The First Structural and Mechanistic Insights for Class D beta-Lactamases: Evidence for a Novel Catalytic Process for Turnover of beta-Lactam Antibiotics
Authors: Golemi, D. / Maveyraud, L. / Vakulenko, S. / Tranier, S. / Ishiwata, A. / Kotra, L.P. / Samama, J.P. / Mobashery, S.
History
DepositionApr 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA LACTAMASE OXA-10
B: BETA LACTAMASE OXA-10
C: BETA LACTAMASE OXA-10
D: BETA LACTAMASE OXA-10


Theoretical massNumber of molelcules
Total (without water)110,0974
Polymers110,0974
Non-polymers00
Water8,305461
1
A: BETA LACTAMASE OXA-10
C: BETA LACTAMASE OXA-10


Theoretical massNumber of molelcules
Total (without water)55,0492
Polymers55,0492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-9 kcal/mol
Surface area19920 Å2
MethodPISA
2
B: BETA LACTAMASE OXA-10
D: BETA LACTAMASE OXA-10


Theoretical massNumber of molelcules
Total (without water)55,0492
Polymers55,0492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-9 kcal/mol
Surface area19780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.415, 82.395, 101.488
Angle α, β, γ (deg.)90.00, 95.40, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a homodimer. There are two such dimers in the asymmetric unit. One functional assembly is constructed from chain A and a symmetry partner of chain C. The second dimer is constructed from chain B and a symmetry partner of chain D. The symmetry transformation that applies to chain C is: 1.00000 0.00000 0.00000 -66.41500 0.00000 1.00000 0.00000 0.00000 0.00000 0.00000 1.00000 0.00000 The symmetry transformation that applies to chain D is: -1.00000 0.00000 0.00000 -19.10086 0.00000 1.00000 0.00000 41.19710 0.00000 0.00000 -1.00000 202.07501

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Components

#1: Protein
BETA LACTAMASE OXA-10 / OXA-10


Mass: 27524.291 Da / Num. of mol.: 4 / Fragment: FULL LENGTH FUNCTIONAL ENZYME
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Plasmid: PET24A+ / Production host: Escherichia coli (E. coli) / References: UniProt: P14489, beta-lactamase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 461 / 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: 2.51 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 8.5
Details: ammonium sulfate, Tris, pH 8.5, EVAPORATION, temperature 277K
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.83996
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 6, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.83996 Å / Relative weight: 1
ReflectionResolution: 2.4→31.22 Å / Num. all: 41455 / Num. obs: 41455 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 32.7 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 9.2
Reflection shellResolution: 2.4→2.55 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.067 / Num. unique all: 5619 / % possible all: 91.7
Reflection
*PLUS

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementResolution: 2.4→31.22 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 2101 -RANDOM
Rwork0.187 ---
all0.19 41436 --
obs0.19 41436 98.3 %-
Refinement stepCycle: LAST / Resolution: 2.4→31.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7569 0 0 461 8030
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.008
X-RAY DIFFRACTIONo_angle_deg1.9
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
σ(F): 0 / Rfactor all: 0.19 / Rfactor obs: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_plane_restr0.007

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