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- PDB-1k38: CRYSTAL STRUCTURE OF THE CLASS D BETA-LACTAMASE OXA-2 -

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Basic information

Entry
Database: PDB / ID: 1k38
TitleCRYSTAL STRUCTURE OF THE CLASS D BETA-LACTAMASE OXA-2
ComponentsBeta-lactamase OXA-2
KeywordsHYDROLASE / serine beta-lactamase / antibiotic resistance / carbamylated lysine
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Beta-lactamase OXA-2
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKerff, F. / Fonze, E. / Bouillenne, F. / Frere, J.M. / Charlier, P.
Citation
Journal: To be Published
Title: CRYSTAL STRUCTURE OF THE CLASS D BETA-LACTAMASE OXA-2
Authors: Kerff, F. / Fonze, E. / Bouillenne, F. / Frere, J.M. / Charlier, P.
#1: Journal: BIOCHEM.J. / Year: 1993
Title: Substrate inactivation of the OXA2 beta-lactamase
Authors: Ledent, P. / Frere, J.M.
#2: Journal: BIOCHEM.J. / Year: 1993
Title: A comparative study of class-D beta-lactamase
Authors: Ledent, P. / Raquet, X. / Joris, B. / Van Beumen, J. / Frere, J.M.
History
DepositionOct 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 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-2
B: Beta-lactamase OXA-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0335
Polymers58,8952
Non-polymers1383
Water5,657314
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.979, 106.899, 129.168
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-543-

HOH

Detailsthe biological assembly is a monomer or a dimer depending on conditions

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Components

#1: Protein Beta-lactamase OXA-2 / Penicillinase


Mass: 29447.264 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: oxa-2 / Plasmid: pDML303 / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: P0A1V8, beta-lactamase
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.31 Å3/Da / Density % sol: 46.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: sodium formate, bicine, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 7, 2000
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→25.08 Å / Num. all: 86412 / Num. obs: 86412 / % possible obs: 89.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 19.1 Å2 / Rsym value: 0.044 / Net I/σ(I): 10.4
Reflection shellResolution: 1.45→1.49 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 2 / Num. unique all: 3140 / Rsym value: 0.297 / % possible all: 50.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K4F, STRUCTURE OF OXA-10

1k4f


Resolution: 1.5→25.08 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2683187.98 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.211 8115 10 %RANDOM
Rwork0.198 ---
all-80903 --
obs-80903 92.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.295 Å2 / ksol: 0.392708 e/Å3
Displacement parametersBiso mean: 22.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20 Å20 Å2
2--4.93 Å20 Å2
3----5.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.5→25.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3949 0 0 323 4272
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it1.161.5
X-RAY DIFFRACTIONc_mcangle_it1.852
X-RAY DIFFRACTIONc_scbond_it1.842
X-RAY DIFFRACTIONc_scangle_it2.742.5
LS refinement shellResolution: 1.5→1.55 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.335 630 9.8 %
Rwork0.287 5830 -
obs-5830 74.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_PSE.PARAMPROTEIN-PSE.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4FMT.PARAMFMT.TOP

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