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- PDB-5boh: Crystal Structure of OXA-58 with the Substrate-Binding Cleft in a... -

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Basic information

Entry
Database: PDB / ID: 5boh
TitleCrystal Structure of OXA-58 with the Substrate-Binding Cleft in a Closed State
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta-lactamase / carbapenem / multi-drug resistance / carbamic acid
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 / 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: 1.8 Å
AuthorsSaino, H. / Sugiyabu, T. / Miyano, M.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Scienc15K21356 Japan
MEXT-Supported Program for the Strategic Research Foundation at Private UniversitiesS1311005 Japan
CitationJournal: Plos One / Year: 2015
Title: Crystal Structure of OXA-58 with the Substrate-Binding Cleft in a Closed State: Insights into the Mobility and Stability of the OXA-58 Structure
Authors: Saino, H. / Sugiyabu, T. / Ueno, G. / Yamamoto, M. / Ishii, Y. / Miyano, M.
History
DepositionMay 27, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Data collection
Revision 1.2Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 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 1.4Nov 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8752
Polymers28,7791
Non-polymers961
Water2,666148
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-4 kcal/mol
Surface area10780 Å2
2
A: Beta-lactamase
hetero molecules

A: Beta-lactamase
hetero molecules

A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,6256
Polymers86,3373
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area4460 Å2
ΔGint-65 kcal/mol
Surface area28130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.290, 75.290, 120.682
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Beta-lactamase /


Mass: 28778.896 Da / Num. of mol.: 1 / Mutation: 43 N-term residues truncated, UNP residues 44-280
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: blaOXA-58, bla-oxa-58, bla-oxa58 / Plasmid: pColdI / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q2TR58, beta-lactamase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.23 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M MOPS pH 7.0, 1.5M Li2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Dec 14, 2013 / Details: remote measurements
RadiationMonochromator: Fixed exit Si double crystal monochromator, Si (111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→28.68 Å / Num. obs: 47274 / % possible obs: 100 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 5.7
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLM7.0.9data processing
SCALA3.3.20data reduction
SCALA3.3.20data scaling
PHASER2.5.3phasing
Coot0.8model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OH0

4oh0


Resolution: 1.8→28.68 Å / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 17.6 / Stereochemistry target values: TWIN_LSQ_F
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.1689 3992 8.44 %
Rwork0.149 --
obs0.1584 47274 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→28.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1896 0 5 148 2049
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071944
X-RAY DIFFRACTIONf_angle_d1.122629
X-RAY DIFFRACTIONf_dihedral_angle_d16.156713
X-RAY DIFFRACTIONf_chiral_restr0.066281
X-RAY DIFFRACTIONf_plane_restr0.008338
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8008-1.86510.23414000.21974282X-RAY DIFFRACTION91
1.8651-1.93970.20694040.20374352X-RAY DIFFRACTION92
1.9397-2.0280.21044020.19074338X-RAY DIFFRACTION92
2.028-2.13480.20353840.18324302X-RAY DIFFRACTION92
2.1348-2.26850.19044100.1714348X-RAY DIFFRACTION91
2.2685-2.44350.18833960.16724300X-RAY DIFFRACTION92
2.4435-2.68910.17194100.15874388X-RAY DIFFRACTION91
2.6891-3.07760.18233880.16254252X-RAY DIFFRACTION92
3.0776-3.87480.16763940.13654360X-RAY DIFFRACTION92
3.8748-24.14820.13374040.12594322X-RAY DIFFRACTION91

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