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- PDB-9cv4: Crystal structure of the metallo-beta-lactamase VIM-31 with D-cap... -

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Basic information

Entry
Database: PDB / ID: 9cv4
TitleCrystal structure of the metallo-beta-lactamase VIM-31 with D-captopril
ComponentsMetallo-beta-lactamase type 2
KeywordsHYDROLASE / metallo-beta-lactamase
Function / homology: / : / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / metal ion binding / Chem-MCO / VIM-31
Function and homology information
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsSilwal, S.B. / Nix, J.C. / Page, R.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)128595 United States
CitationJournal: J.Inorg.Biochem. / Year: 2025
Title: Mutation of an active site-adjacent residue in VIM indirectly dictates interactions with and blunts inhibition by D-captopril.
Authors: Silwal, S.B. / Wamsley, B. / Wang, Z. / Gung, B.W. / Nix, J.C. / Page, R.C.
History
DepositionJul 28, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2735
Polymers25,8601
Non-polymers4144
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.580, 77.140, 79.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-524-

HOH

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Components

#1: Protein Metallo-beta-lactamase type 2 / B2 metallo-beta-lactamase / Metallo-beta-lactamase type II


Mass: 25859.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: blaVIM-31 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I3RJZ3, beta-lactamase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MCO / 1-(3-MERCAPTO-2-METHYL-PROPIONYL)-PYRROLIDINE-2-CARBOXYLIC ACID


Mass: 217.285 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15NO3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.99 Å3/Da / Density % sol: 38.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Magnesium Chloride, 0.1 M HEPES, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00001 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 1.36→39.51 Å / Num. obs: 78569 / % possible obs: 94.31 % / Redundancy: 4.6 % / Biso Wilson estimate: 17.55 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05247 / Rpim(I) all: 0.02523 / Rrim(I) all: 0.05839 / Net I/σ(I): 13.13
Reflection shellResolution: 1.36→1.4 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.4901 / Num. unique obs: 2324 / CC1/2: 0.62 / Rpim(I) all: 0.4746 / Rrim(I) all: 0.6831 / % possible all: 50.93

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.36→39.51 Å / SU ML: 0.1354 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.8423
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1977 2003 4.8 %
Rwork0.1784 39683 -
obs0.1793 41686 94.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.88 Å2
Refinement stepCycle: LAST / Resolution: 1.36→39.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1744 0 17 137 1898
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00631802
X-RAY DIFFRACTIONf_angle_d0.96372467
X-RAY DIFFRACTIONf_chiral_restr0.0819284
X-RAY DIFFRACTIONf_plane_restr0.0069325
X-RAY DIFFRACTIONf_dihedral_angle_d12.7067631
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.40.3563730.31561513X-RAY DIFFRACTION50.93
1.4-1.440.27551190.24372399X-RAY DIFFRACTION80.09
1.44-1.480.22841350.19612692X-RAY DIFFRACTION90.78
1.48-1.530.21341470.1832887X-RAY DIFFRACTION97.93
1.53-1.580.21821530.17263004X-RAY DIFFRACTION100
1.58-1.640.18781500.17292954X-RAY DIFFRACTION99.97
1.64-1.720.21031470.18852987X-RAY DIFFRACTION99.97
1.72-1.810.19571570.17742978X-RAY DIFFRACTION100
1.81-1.920.17771480.17553018X-RAY DIFFRACTION99.97
1.92-2.070.20011500.17492982X-RAY DIFFRACTION99.97
2.07-2.280.19911580.18132997X-RAY DIFFRACTION99.87
2.28-2.610.19311470.1843045X-RAY DIFFRACTION99.97
2.61-3.290.20351560.18443051X-RAY DIFFRACTION100
3.29-39.510.18651630.1653176X-RAY DIFFRACTION99.88
Refinement TLS params.Method: refined / Origin x: -18.4981944018 Å / Origin y: -18.3067854519 Å / Origin z: -10.8223256534 Å
111213212223313233
T0.0788973540524 Å2-0.00634399120294 Å20.00366350932834 Å2-0.102442244658 Å2-0.0153531949286 Å2--0.0979637515921 Å2
L1.71013287273 °2-0.162167031264 °2-0.290068699138 °2-2.12809596135 °2-0.246682666204 °2--3.03767834673 °2
S0.0630224196119 Å °-0.0821876080202 Å °0.117217762419 Å °0.058400511516 Å °0.0243975953751 Å °-0.0191640055652 Å °-0.0407880879846 Å °0.157073388742 Å °-0.0543390935389 Å °
Refinement TLS groupSelection details: all

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