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- PDB-7vvi: OXA-58 crystal structure of acylated meropenem complex -

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Basic information

Entry
Database: PDB / ID: 7vvi
TitleOXA-58 crystal structure of acylated meropenem complex
ComponentsBeta-lactamase
KeywordsHYDROLASE / OXA / multi-drug resistance / Complex / Degradation
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic / plasma membrane
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/transpeptidase-like / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Chem-MER / Beta-lactamase OXA-58
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSaino, H. / Sugiyabu, T. / Miyano, M.
Funding support Japan, 2items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)S1311005 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)18K07118 Japan
Citation
Journal: to be published
Title: OXA-58 crystal structure of acylated meropenem complex
Authors: Saino, H. / Okimoto, N. / Otsuka, T. / Sugiyabu, T. / Sasaki, I. / Ueno, G. / Oouchi, M. / Yamamoto, M. / Ishii, K. / Taiji, M. / Miyano, M.
#1: Journal: 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
DepositionNov 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2603
Polymers28,7791
Non-polymers4822
Water6,882382
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-5 kcal/mol
Surface area10700 Å2
Unit cell
Length a, b, c (Å)75.380, 75.380, 119.531
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

#1: Protein Beta-lactamase


Mass: 28778.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: blaOXA-58, bla-oxa-58, bla-oxa58 / Plasmid: pCold I / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2TR58, beta-lactamase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MER / (4R,5S)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-d ihydro-1H-pyrrole-2-carboxylic acid / Meropenem, bound form


Mass: 385.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O5S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.27 Å3/Da / Density % sol: 45.87 % / Description: Thin plate
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: LiSO4, HEPES-Na, Meropenem soaking

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→19.29 Å / Num. obs: 685938 / % possible obs: 99.52 % / Redundancy: 6.9 % / Biso Wilson estimate: 12.56 Å2 / CC1/2: 0.628 / CC star: 0.878 / Rmerge(I) obs: 0.7342 / Rpim(I) all: 0.2962 / Rsym value: 0.794 / Net I/σ(I): 158.17
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.7758 / Mean I/σ(I) obs: 18.01 / Num. unique obs: 66353 / CC1/2: 0.132 / CC star: 0.482 / Rpim(I) all: 0.3234 / Rrim(I) all: 0.8451 / % possible all: 99.37

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BOH

5boh


Resolution: 1.4→19.29 Å / Cross valid method: FREE R-VALUE / σ(F): 1.27 / Phase error: 16.3904
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1486 3992 4.02 %
Rwork0.1446 95268 -
obs0.1583 99260 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.51 Å2
Refinement stepCycle: LAST / Resolution: 1.4→19.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1896 0 31 382 2309
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01071971
X-RAY DIFFRACTIONf_angle_d1.4272668
X-RAY DIFFRACTIONf_chiral_restr0.0868287
X-RAY DIFFRACTIONf_plane_restr0.0061341
X-RAY DIFFRACTIONf_dihedral_angle_d16.3553764
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.25991930.2574715X-RAY DIFFRACTION95.56
1.42-1.450.26212050.24714772X-RAY DIFFRACTION95.17
1.45-1.480.24021960.24214764X-RAY DIFFRACTION95.51
1.48-1.510.19971930.23244737X-RAY DIFFRACTION95.66
1.51-1.540.2261970.23494781X-RAY DIFFRACTION95.66
1.54-1.580.20351990.21764733X-RAY DIFFRACTION95.5
1.58-1.620.20062060.21264766X-RAY DIFFRACTION95.43
1.62-1.660.21472000.20584775X-RAY DIFFRACTION95.54
1.66-1.710.17981990.19874753X-RAY DIFFRACTION95.6
1.71-1.760.19471960.20214745X-RAY DIFFRACTION95.63
1.76-1.830.19932080.20264753X-RAY DIFFRACTION95.44
1.83-1.90.18672000.19444835X-RAY DIFFRACTION95.74
1.9-1.990.15712010.18074751X-RAY DIFFRACTION95.67
1.99-2.090.14862050.17524790X-RAY DIFFRACTION95.57
2.09-2.220.15211970.15434776X-RAY DIFFRACTION95.79
2.22-2.390.1592050.15194771X-RAY DIFFRACTION95.57
2.39-2.630.15271940.154729X-RAY DIFFRACTION95.81
2.63-3.010.17262100.12494769X-RAY DIFFRACTION95.46
3.01-3.790.11741880.1084823X-RAY DIFFRACTION96
3.79-19.290.11031810.1114749X-RAY DIFFRACTION95.02

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