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- PDB-7vx3: OXA-58 crystal structure of acylated meropenem complex 2 -

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Basic information

Entry
Database: PDB / ID: 7vx3
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: 1.8 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
Water3,711206
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 area10590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.290, 75.290, 119.470
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
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (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.: 206 / 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: 2.07 Å3/Da / Density % sol: 40.55 % / Description: Thin plate
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES-Na (pH 7.5), 1.55 M LiSO4, NaCO3

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: flash cooling / 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 5, 2014 / Details: confocal mirror
RadiationMonochromator: Ni-filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→28.62 Å / Num. obs: 184659 / % possible obs: 99.95 % / Redundancy: 7.9 % / Biso Wilson estimate: 17.59 Å2 / CC1/2: 0.587 / CC star: 0.86 / Net I/σ(I): 65.48
Reflection shellResolution: 1.8→1.864 Å / Redundancy: 7.6 % / Num. unique obs: 17814 / CC1/2: 0.371 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
iMOSFLMdata reduction
MOLREPphasing
CrystalCleardata collection
iMOSFLMdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VVI

7vvi


Resolution: 1.8→28.62 Å / Cross valid method: FREE R-VALUE / σ(F): 1.13 / Phase error: 19.2616
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1629 3982 8.68 %
Rwork0.1457 41880 -
obs0.1694 45862 97.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.43 Å2
Refinement stepCycle: LAST / Resolution: 1.8→28.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1896 0 57 206 2159
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00352025
X-RAY DIFFRACTIONf_angle_d0.92442746
X-RAY DIFFRACTIONf_chiral_restr0.0469300
X-RAY DIFFRACTIONf_plane_restr0.0045346
X-RAY DIFFRACTIONf_dihedral_angle_d17.0906866
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.830.2881920.3562141X-RAY DIFFRACTION91.03
1.83-1.860.34341970.30282124X-RAY DIFFRACTION90.77
1.86-1.90.26952040.27612138X-RAY DIFFRACTION90.13
1.9-1.940.32671930.26122066X-RAY DIFFRACTION90.53
1.94-1.980.29361980.23032174X-RAY DIFFRACTION90.58
1.98-2.030.25481970.21312120X-RAY DIFFRACTION90.06
2.03-2.080.221890.20732068X-RAY DIFFRACTION90.31
2.08-2.130.24841960.19082117X-RAY DIFFRACTION90.16
2.13-2.20.24131970.18532088X-RAY DIFFRACTION89.77
2.2-2.270.18571950.18732153X-RAY DIFFRACTION89.71
2.27-2.350.19491870.17342078X-RAY DIFFRACTION89.65
2.35-2.440.17271940.17632091X-RAY DIFFRACTION89.59
2.44-2.550.18771920.16062081X-RAY DIFFRACTION89.39
2.55-2.690.18552060.16312124X-RAY DIFFRACTION88.94
2.69-2.860.17371930.15712024X-RAY DIFFRACTION88.62
2.86-3.080.19861960.15182094X-RAY DIFFRACTION88.88
3.08-3.380.17912000.13862085X-RAY DIFFRACTION88.87
3.39-3.870.14571940.12432052X-RAY DIFFRACTION88.22
3.88-4.870.12631980.10712075X-RAY DIFFRACTION87.85
4.89-28.620.1291850.1482066X-RAY DIFFRACTION87.99

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