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- PDB-7vx6: OXA-58 crystal structure of acylated meropenem complex 2 -

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Basic information

Entry
Database: PDB / ID: 7vx6
TitleOXA-58 crystal structure of acylated meropenem complex 2
ComponentsBeta-lactamase
KeywordsHYDROLASE / OXA / multi-drug resistance / complex / degradation / ANTIBIOTIC
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / 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/transpeptidase-like / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Chem-DWZ / Chem-MER / Beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 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 2
Authors: Saino, H. / Sugiyabu, T. / 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 12, 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

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3654
Polymers31,4981
Non-polymers8673
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-10 kcal/mol
Surface area10530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.240, 75.240, 119.600
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: 31498.209 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 B (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: Chemical ChemComp-DWZ / (2S,3R,4S)-4-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-3,4-dihydro-2H-pyrrole-5-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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 40.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.60 M LiSO4, 0.1 M HEPES-Na (pH7.5), Meropenem

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Jun 4, 2014
RadiationMonochromator: Ni-filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→24.12 Å / Num. obs: 27801 / % possible obs: 99.97 % / Redundancy: 9.4 % / CC1/2: 0.75 / Net I/σ(I): 88.71
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 9.1 % / Num. unique obs: 2786 / CC1/2: 0.65 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
iMOSFLM1data reduction
CrystalCleardata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VVI

7vvi


Resolution: 1.7→24.12 Å / Cross valid method: FREE R-VALUE / σ(F): 1.11 / Phase error: 19.5849
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.167 3980 7.17 %
Rwork0.1417 51546 -
obs0.1615 27801 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.03 Å2
Refinement stepCycle: LAST / Resolution: 1.7→24.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1896 0 57 253 2206
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00471998
X-RAY DIFFRACTIONf_angle_d0.88732707
X-RAY DIFFRACTIONf_chiral_restr0.05294
X-RAY DIFFRACTIONf_plane_restr0.0055343
X-RAY DIFFRACTIONf_dihedral_angle_d12.6906362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.730.33862050.30292587X-RAY DIFFRACTION92.06
1.73-1.760.29062020.2482558X-RAY DIFFRACTION92.61
1.76-1.790.25222060.24272624X-RAY DIFFRACTION92.66
1.79-1.830.26631940.22772538X-RAY DIFFRACTION92.83
1.83-1.870.24511920.2172588X-RAY DIFFRACTION93.09
1.87-1.910.23922020.19012598X-RAY DIFFRACTION92.72
1.91-1.960.24782000.19462635X-RAY DIFFRACTION92.91
1.96-2.020.2131940.18232487X-RAY DIFFRACTION92.66
2.02-2.070.18241890.18872595X-RAY DIFFRACTION93.08
2.07-2.140.1852080.18092582X-RAY DIFFRACTION92.41
2.14-2.220.19751980.17532595X-RAY DIFFRACTION92.74
2.22-2.310.18831960.18032516X-RAY DIFFRACTION92.64
2.31-2.410.19982010.17072584X-RAY DIFFRACTION92.62
2.41-2.540.19122080.15672574X-RAY DIFFRACTION92.39
2.54-2.70.16031960.15552603X-RAY DIFFRACTION92.9
2.7-2.910.17581980.1532588X-RAY DIFFRACTION92.83
2.91-3.20.16811970.14832539X-RAY DIFFRACTION92.6
3.2-3.660.16512020.12662596X-RAY DIFFRACTION92.65
3.66-4.610.14331860.10582573X-RAY DIFFRACTION93.09
4.61-24.120.16712010.12482591X-RAY DIFFRACTION92.6

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