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- PDB-6nz8: Structure of carbamylated apo OXA-231 carbapenemase -

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Basic information

Entry
Database: PDB / ID: 6nz8
TitleStructure of carbamylated apo OXA-231 carbapenemase
ComponentsBeta-lactamase OXA-231
KeywordsHYDROLASE / beta-lactamase / oxacillinase / OXA-143 subgroup / carbapenemase
Function / homologyPenicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / penicillin binding / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta / Beta-lactamase OXA-231
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsFavaro, D.C. / Llontop, E.E. / Vasconcelos, F.N. / Antunes, V.U. / Farah, S.C. / Lincopan, N.
CitationJournal: Biochemistry / Year: 2019
Title: Importance of the beta 5-beta 6 Loop for the Structure, Catalytic Efficiency, and Stability of Carbapenem-Hydrolyzing Class D beta-Lactamase Subfamily OXA-143.
Authors: Antunes, V.U. / Llontop, E.E. / Vasconcelos, F.N.D.C. / Lopez de Los Santos, Y. / Oliveira, R.J. / Lincopan, N. / Farah, C.S. / Doucet, N. / Mittermaier, A. / Favaro, D.C.
History
DepositionFeb 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 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-231
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6014
Polymers29,5071
Non-polymers943
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.786, 54.786, 96.243
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Beta-lactamase OXA-231 / Carbapenem-hydrolyzing class D beta-lactamase / OXA-143 family carbapenem-hydrolyzing class D beta- ...Carbapenem-hydrolyzing class D beta-lactamase / OXA-143 family carbapenem-hydrolyzing class D beta-lactamase OXA-231


Mass: 29506.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: blaOXA-231, bla-OXA-231, C3415_08220 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: H9U2W6
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 1.78 Å3/Da / Density % sol: 30.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0,1 M Tris pH 8,5; 2,0 M Ammonium Sulfate, 50 mM sodium phosphate; 25 mM sodium bicarbonate; 25 mM sodium sulfate; sodium chloride.
PH range: 7.0-8.5

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Data collection

DiffractionMean temperature: 104.9 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 65867 / % possible obs: 98.36 % / Redundancy: 12 % / Biso Wilson estimate: 15.92 Å2 / Rmerge(I) obs: 0.01269 / Rrim(I) all: 0.01795 / Net I/σ(I): 23.68
Reflection shellResolution: 1.2→1.38 Å / Num. unique obs: 6377 / % possible all: 96.01

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JC7
Resolution: 1.2→36.77 Å / SU ML: 0.126 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.7154
RfactorNum. reflection% reflectionSelection details
Rfree0.1944 2000 3.04 %0.2
Rwork0.1669 ---
obs0.1677 65846 98.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 25.923 Å2
Refinement stepCycle: LAST / Resolution: 1.2→36.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1840 0 3 161 2004
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00781997
X-RAY DIFFRACTIONf_angle_d0.95932715
X-RAY DIFFRACTIONf_chiral_restr0.0813296
X-RAY DIFFRACTIONf_plane_restr0.0075351
X-RAY DIFFRACTIONf_dihedral_angle_d24.6515753
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.230.32031360.2934335X-RAY DIFFRACTION94.64
1.23-1.260.31311430.25874534X-RAY DIFFRACTION99.47
1.26-1.30.28051420.2374562X-RAY DIFFRACTION99.3
1.3-1.340.29091410.22364502X-RAY DIFFRACTION98.39
1.34-1.390.2371410.22024495X-RAY DIFFRACTION98.14
1.39-1.440.2261430.18394561X-RAY DIFFRACTION99.41
1.44-1.510.20561430.16464563X-RAY DIFFRACTION98.87
1.51-1.590.18481390.164466X-RAY DIFFRACTION97.05
1.59-1.690.18821440.15614586X-RAY DIFFRACTION99.56
1.69-1.820.18791440.15044592X-RAY DIFFRACTION98.77
1.82-20.1611420.154540X-RAY DIFFRACTION97.83
2-2.290.17621450.14984650X-RAY DIFFRACTION99.58
2.29-2.890.21131440.17034605X-RAY DIFFRACTION97.48
2.89-36.790.18021530.16134858X-RAY DIFFRACTION98.62

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