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- PDB-3dw0: Crystal structure of the class A carbapenemase KPC-2 at 1.6 angst... -

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Basic information

Entry
Database: PDB / ID: 3dw0
TitleCrystal structure of the class A carbapenemase KPC-2 at 1.6 angstrom resolution
ComponentsClass A carbapenemase KPC-2
KeywordsHYDROLASE / beta-lactamase / KPC-2 / carbapenemase / Antibiotic resistance
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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsPetrella, S. / Ziental-Gelus, N. / Mayer, C. / Jarlier, V. / Sougakoff, W.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2008
Title: Genetic and structural insights into the dissemination potential of the extremely broad-spectrum class A beta-lactamase KPC-2 identified in an Escherichia coli strain and an Enterobacter ...Title: Genetic and structural insights into the dissemination potential of the extremely broad-spectrum class A beta-lactamase KPC-2 identified in an Escherichia coli strain and an Enterobacter cloacae strain isolated from the same patient in France.
Authors: Petrella, S. / Ziental-Gelus, N. / Mayer, C. / Renard, M. / Jarlier, V. / Sougakoff, W.
History
DepositionJul 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
SupersessionSep 16, 2008ID: 2ODS
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Oct 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: Class A carbapenemase KPC-2
B: Class A carbapenemase KPC-2


Theoretical massNumber of molelcules
Total (without water)62,5452
Polymers62,5452
Non-polymers00
Water5,513306
1
A: Class A carbapenemase KPC-2


Theoretical massNumber of molelcules
Total (without water)31,2721
Polymers31,2721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Class A carbapenemase KPC-2


Theoretical massNumber of molelcules
Total (without water)31,2721
Polymers31,2721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.300, 91.300, 73.100
Angle α, β, γ (deg.)90.00, 112.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Class A carbapenemase KPC-2


Mass: 31272.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: 2138 / Plasmid: pET29 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A8DS27
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.77 Å3/Da / Density % sol: 55.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20% PEG 6000, 0.1 M KSCN, 0.1 M Sodium Acetate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 24, 2006 / Details: mirror 1, double crystal, mirror 2
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→19.76 Å / Num. obs: 86680 / % possible obs: 96.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 14.2 Å2 / Rsym value: 0.05 / Net I/σ(I): 21.54
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 3 % / Mean I/σ(I) obs: 11.68 / Num. unique all: 14100 / Rsym value: 0.137 / % possible all: 95.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
Xnemodata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1DY6

1dy6


Resolution: 1.6→19.76 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.92 / SU B: 2.667 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2108 4335 5 %RANDOM
Rwork0.18758 ---
obs0.18875 82347 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.889 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0.22 Å2
2--0.36 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3953 0 0 306 4259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224031
X-RAY DIFFRACTIONr_angle_refined_deg1.2551.9585483
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4785523
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.88623.69168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.95315618
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1251530
X-RAY DIFFRACTIONr_chiral_restr0.0840.2619
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023086
X-RAY DIFFRACTIONr_nbd_refined0.2320.21988
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22835
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0960.2270
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.284
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0740.220
X-RAY DIFFRACTIONr_mcbond_it0.9361.52660
X-RAY DIFFRACTIONr_mcangle_it1.37524153
X-RAY DIFFRACTIONr_scbond_it2.12531549
X-RAY DIFFRACTIONr_scangle_it3.0594.51330
X-RAY DIFFRACTIONr_rigid_bond_restr1.18534209
X-RAY DIFFRACTIONr_sphericity_free4.6543306
X-RAY DIFFRACTIONr_sphericity_bonded2.35333953
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 307 -
Rwork0.184 5819 -
obs--100 %

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