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- PDB-2jc7: The crystal structure of the carbapenemase OXA-24 reveals new ins... -

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Basic information

Entry
Database: PDB / ID: 2jc7
TitleThe crystal structure of the carbapenemase OXA-24 reveals new insights into the mechanism of carbapenem-hydrolysis
ComponentsBETA-LACTAMASE OXA-24
KeywordsHYDROLASE / PLASMID / B-LACTAMASES / ENZYME MECHANISM / CARBAPENEM RESISTANCE
Function / homology
Function and homology information


penicillin binding / beta-lactamase activity
Similarity search - Function
Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesACINETOBACTER BAUMANNII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSantillana, E. / Romero, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: Crystal Structure of the Carbapenemase Oxa-24 Reveals Insights Into the Mechanism of Carbapenem Hydrolysis.
Authors: Santillana, E. / Beceiro, A. / Bou, G. / Romero, A.
History
DepositionDec 20, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-LACTAMASE OXA-24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6402
Polymers27,5441
Non-polymers961
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)102.200, 102.200, 86.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein BETA-LACTAMASE OXA-24 / OXA40 / CARBAPENEM-HYDROLYZING BETA-LACTAMASE OXA-40 / BETA-LACTAMASE / OXA-24 CARBAPENEMASE


Mass: 27543.658 Da / Num. of mol.: 1 / Fragment: RESIDUES 32-275
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACINETOBACTER BAUMANNII (bacteria) / Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8RLA6, beta-lactamase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 1 TO 21 COMPRISED THE SIGNAL PEPTIDE AND ARE NOT PRESENT IN THE RECOMBINANT PROTEIN ...RESIDUES 1 TO 21 COMPRISED THE SIGNAL PEPTIDE AND ARE NOT PRESENT IN THE RECOMBINANT PROTEIN EXPRESSED TO OBTAIN THE 3D STRUCTURE.PROTEIN_ID: CAB92323, EMBL NUCLEOTIDE ACCESSION NUMBER: AJ239129

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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: 4.09 Å3/Da / Density % sol: 68.75 %
Crystal growDetails: 0.1 M BIS-TRIS PH 6.5, 2 M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.979
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→55 Å / Num. obs: 16630 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 13.9 % / Biso Wilson estimate: 36.4 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.4
Reflection shellResolution: 2.48→2.62 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 2.9 / % possible all: 96.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K57

1k57


Resolution: 2.5→15 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1439570.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1266 7.8 %RANDOM
Rwork0.192 ---
obs0.192 16213 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.4546 Å2 / ksol: 0.384349 e/Å3
Displacement parametersBiso mean: 32.1 Å2
Baniso -1Baniso -2Baniso -3
1--8.62 Å20 Å20 Å2
2---8.62 Å20 Å2
3---17.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1932 0 5 121 2058
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.341.5
X-RAY DIFFRACTIONc_mcangle_it2.242
X-RAY DIFFRACTIONc_scbond_it2.332
X-RAY DIFFRACTIONc_scangle_it3.432.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.296 205 7.7 %
Rwork0.234 2443 -
obs--99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP

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