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- PDB-3g4p: OXA-24 beta-lactamase at pH 7.5 -

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Basic information

Entry
Database: PDB / ID: 3g4p
TitleOXA-24 beta-lactamase at pH 7.5
ComponentsBeta-lactamase OXA-24
KeywordsHYDROLASE / 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: 1.97 Å
AuthorsSantillana, E. / Romero, A.
Citation
Journal: J.Am.Chem.Soc. / Year: 2010
Title: Design, synthesis, and crystal structures of 6-alkylidene-2'-substituted penicillanic acid sulfones as potent inhibitors of Acinetobacter baumannii OXA-24 carbapenemase
Authors: Bou, G. / Santillana, E. / Sheri, A. / Beceiro, A. / Sampson, J.M. / Kalp, M. / Bethel, C.R. / Distler, A.M. / Drawz, S.M. / Pagadala, S.R. / van den Akker, F. / Bonomo, R.A. / Romero, A. / Buynak, J.D.
#1: Journal: 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
DepositionFeb 4, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 23, 2010Provider: 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase OXA-24


Theoretical massNumber of molelcules
Total (without water)27,5871
Polymers27,5871
Non-polymers00
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.310, 102.310, 84.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-301-

HOH

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Components

#1: Protein Beta-lactamase OXA-24 / Beta-lactamase OXA-33 / Oxa40 / Carbapenem-hydrolyzing beta-lactamase OXA-40 / Beta-lactamase


Mass: 27586.660 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 32-275
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: oxa-24 / Plasmid: PGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q8RLA6, beta-lactamase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 3.98 Å3/Da / Density % sol: 69.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M SODIUM ACETATE, 28% PEG 2000 MME, 0.1M HEPES (PH 7.5), VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 14, 2008
RadiationMonochromator: SINGLE SILICON (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.97→31.59 Å / Num. all: 32135 / Num. obs: 32064 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Biso Wilson estimate: 24.04 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 7.2
Reflection shellResolution: 1.97→2.08 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 1.5 / Num. unique all: 4548 / % possible all: 99.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2jc7

2jc7


Resolution: 1.97→30.95 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.702 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24408 1619 5.1 %RANDOM
Rwork0.19685 ---
all0.1995 32135 --
obs0.19917 30384 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.97→30.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1939 0 0 167 2106
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.0221977
X-RAY DIFFRACTIONr_angle_refined_deg2.4791.9572666
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.395243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.71225.56888
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.40515374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.878157
X-RAY DIFFRACTIONr_chiral_restr0.1770.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021464
X-RAY DIFFRACTIONr_nbd_refined0.2330.2906
X-RAY DIFFRACTIONr_nbtor_refined0.3190.21376
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2130
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.214
X-RAY DIFFRACTIONr_mcbond_it1.9241.51257
X-RAY DIFFRACTIONr_mcangle_it2.77421945
X-RAY DIFFRACTIONr_scbond_it4.3493851
X-RAY DIFFRACTIONr_scangle_it6.6134.5721
LS refinement shellResolution: 1.97→2.021 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 126 -
Rwork0.321 2148 -
obs--99.3 %

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