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- PDB-2ov5: Crystal structure of the KPC-2 carbapenemase -

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Basic information

Entry
Database: PDB / ID: 2ov5
TitleCrystal structure of the KPC-2 carbapenemase
ComponentsCarbapenemase
KeywordsHYDROLASE / carbapenemase / beta-lactamase
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, 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
beta-lactamase / Carbapenem-hydrolyzing beta-lactamase KPC-2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsKe, W. / Bethel, C.R. / Thomson, J.M. / Bonomo, R.A. / van den Akker, F.
CitationJournal: Biochemistry / Year: 2007
Title: Crystal Structure of KPC-2: Insights into Carbapenemase Activity in Class A beta-Lactamases.
Authors: Ke, W. / Bethel, C.R. / Thomson, J.M. / Bonomo, R.A. / Akker, F.
History
DepositionFeb 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 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: Carbapenemase
B: Carbapenemase
C: Carbapenemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,4826
Polymers82,9923
Non-polymers4903
Water5,296294
1
A: Carbapenemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8272
Polymers27,6641
Non-polymers1631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Carbapenemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8272
Polymers27,6641
Non-polymers1631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Carbapenemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8272
Polymers27,6641
Non-polymers1631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.245, 116.245, 52.001
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Carbapenemase / Class A carbapenemase KPC-2


Mass: 27664.143 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: KPC-2, blaKPC-2 / Plasmid: pBR322 / Species (production host): Escherichia coli
Production host: Escherichia coli str. K-12 substr. DH10B (bacteria)
Strain (production host): DH10B
References: UniProt: Q93LQ9, UniProt: Q9F663*PLUS, beta-lactamase
#2: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.44 Å3/Da / Density % sol: 49.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 16% PEG6000, 0.1M bicine, pH 9, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
Reflection twinType: hemihedral / Operator: h,-h-k,-l / Fraction: 0.42
ReflectionResolution: 1.85→50 Å / Num. obs: 64107 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 19.7
Reflection shellResolution: 1.85→1.92 Å / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 2.3 / % possible all: 90.8

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DY6-A

1dy6


Resolution: 1.85→29.061 Å / Cross valid method: R-free / σ(F): 2573 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.19 2989 5%, random
Rwork0.148 --
obs-61501 -
Solvent computationBsol: 34.797 Å2
Displacement parametersBiso mean: 25.821 Å2
Baniso -1Baniso -2Baniso -3
1-0.232 Å2-0.96 Å20 Å2
2--0.232 Å20 Å2
3----0.463 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.061 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5847 0 33 294 6174
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.006
X-RAY DIFFRACTIONp_angle_d1.288
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3BCN.par
X-RAY DIFFRACTION4cis_peptide.param

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