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- PDB-3c5a: Crystal structure of the C-terminal deleted mutant of the class A... -

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Basic information

Entry
Database: PDB / ID: 3c5a
TitleCrystal structure of the C-terminal deleted mutant of the class A carbapenemase KPC-2 at 1.23 angstrom
ComponentsClass A carbapenemase KPC-2
KeywordsHYDROLASE / beta-lactamase / carbapenemase / C-terminal deleted mutant / Plasmid
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
CITRIC ACID / beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 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 (EBSBL) KPC-2 identified in two strains of Escherichia coli and ...Title: Genetic and structural insights into the dissemination potential of the extremely-broad-spectrum class A {beta}-lactamase (EBSBL) KPC-2 identified in two strains of Escherichia coli and Enterobacter cloacae isolated from the same patient in France
Authors: Petrella, S. / Ziental-Gelus, N. / Mayer, C. / Renard, M. / Jarlier, V. / Sougakoff, W.
History
DepositionJan 31, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 1.3Oct 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1852
Polymers27,9931
Non-polymers1921
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.890, 65.990, 72.130
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 Class A carbapenemase KPC-2 / KPC-2 C-terminal deleted class A beta-lactamase (carbapenemase)


Mass: 27992.506 Da / Num. of mol.: 1 / Fragment: UNP residues 26-289
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET29 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A8DS27
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.04 Å3/Da / Density % sol: 39.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 20% PEG4K, 0.1M KSCN, 0.1M Citrate, VAPOR DIFFUSION, SITTING DROP, pH4.0, temperature 291K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 23, 2007 / 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: 1.23→27.17 Å / Num. obs: 65197 / % possible obs: 97.7 % / Redundancy: 13.6 % / Biso Wilson estimate: 14.7 Å2 / Net I/σ(I): 22.55
Reflection shellResolution: 1.23→1.31 Å / Redundancy: 11.6 % / Mean I/σ(I) obs: 6.5 / Num. unique all: 9747 / Rsym value: 0.196 / % possible all: 91.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
Xnemodata collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ODS

2ods
PDB Unreleased entry


Resolution: 1.23→27.17 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.954 / SU B: 0.644 / SU ML: 0.029 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.196 3259 5 %RANDOM
Rwork0.181 ---
obs0.182 65188 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: 11.796 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.23→27.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1972 0 13 183 2168
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222023
X-RAY DIFFRACTIONr_angle_refined_deg1.1391.9672754
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7395261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.31123.53782
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.72715308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.1341515
X-RAY DIFFRACTIONr_chiral_restr0.0720.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021545
X-RAY DIFFRACTIONr_nbd_refined0.2170.21011
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21414
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2570.2129
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0670.219
X-RAY DIFFRACTIONr_mcbond_it0.5581.51330
X-RAY DIFFRACTIONr_mcangle_it0.93322076
X-RAY DIFFRACTIONr_scbond_it1.3983784
X-RAY DIFFRACTIONr_scangle_it2.074.5678
LS refinement shellResolution: 1.233→1.265 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 212 -
Rwork0.256 4033 -
all-4245 -
obs--100 %

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