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- PDB-9cv1: Crystal structure of the metallo-beta-lactamase VIM-15 with L-cap... -

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Basic information

Entry
Database: PDB / ID: 9cv1
TitleCrystal structure of the metallo-beta-lactamase VIM-15 with L-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 / beta-lactamase / L-CAPTOPRIL / beta-lactamase
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)26,2225
Polymers25,8501
Non-polymers3724
Water3,441191
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.750, 77.510, 79.260
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-501-

HOH

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Components

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


Mass: 25849.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: blaVIM-15 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B4YAJ6, beta-lactamase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-X8Z / L-CAPTOPRIL


Mass: 217.285 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15NO3S / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor, medication*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.01 Å3/Da / Density % sol: 38.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M Magnesium Chloride, 0.1 M Bis-Tris:HCl, 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: 1.072156 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Sep 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072156 Å / Relative weight: 1
ReflectionResolution: 1.29→39.63 Å / Num. obs: 52008 / % possible obs: 98.1 % / Redundancy: 11.6 % / Biso Wilson estimate: 13.31 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.04 / Net I/σ(I): 11
Reflection shellResolution: 1.29→1.34 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 5070 / CC1/2: 0.67 / Rpim(I) all: 0.571 / % possible all: 97.07

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.29→39.63 Å / SU ML: 0.1456 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.6135
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1969 3825 3.84 %
Rwork0.1738 95815 -
obs0.1747 52008 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.82 Å2
Refinement stepCycle: LAST / Resolution: 1.29→39.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1762 0 17 191 1970
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00991845
X-RAY DIFFRACTIONf_angle_d0.92472530
X-RAY DIFFRACTIONf_chiral_restr0.0842291
X-RAY DIFFRACTIONf_plane_restr0.0075334
X-RAY DIFFRACTIONf_dihedral_angle_d14.137647
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.29-1.310.3271280.34543464X-RAY DIFFRACTION95.35
1.31-1.320.39941450.33563477X-RAY DIFFRACTION95.69
1.32-1.340.32641340.28093461X-RAY DIFFRACTION96.43
1.34-1.360.23291310.24423515X-RAY DIFFRACTION96.66
1.36-1.380.26181400.22733571X-RAY DIFFRACTION97.17
1.38-1.40.21821310.22433444X-RAY DIFFRACTION96.94
1.4-1.430.20411530.23283525X-RAY DIFFRACTION97.28
1.43-1.450.23521370.22793531X-RAY DIFFRACTION97.45
1.45-1.480.22771450.20973534X-RAY DIFFRACTION97.53
1.48-1.510.19811410.1923532X-RAY DIFFRACTION97.82
1.51-1.540.19921360.1813544X-RAY DIFFRACTION97.92
1.54-1.570.19931500.17723511X-RAY DIFFRACTION98.1
1.57-1.610.16811290.16883561X-RAY DIFFRACTION98.27
1.61-1.650.20331600.16193540X-RAY DIFFRACTION98.35
1.65-1.690.18881300.15543582X-RAY DIFFRACTION98.62
1.69-1.740.18321470.15443583X-RAY DIFFRACTION98.94
1.74-1.80.14981400.15813611X-RAY DIFFRACTION98.76
1.8-1.860.19761550.1663530X-RAY DIFFRACTION98.74
1.86-1.930.21571410.19633535X-RAY DIFFRACTION97.82
1.93-2.020.19421460.16383586X-RAY DIFFRACTION98.83
2.02-2.130.1691370.15673585X-RAY DIFFRACTION99.55
2.13-2.260.17681490.18053605X-RAY DIFFRACTION99.31
2.26-2.440.2191420.16943563X-RAY DIFFRACTION98.98
2.44-2.680.21771470.16723630X-RAY DIFFRACTION99.95
2.68-3.070.2131420.17843628X-RAY DIFFRACTION100
3.07-3.870.17551540.14963599X-RAY DIFFRACTION99.92
3.87-39.630.16381350.14753568X-RAY DIFFRACTION98.2
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.055644598860.864512163782-0.1687113144373.385332338910.1727474303543.414009049960.0608028347086-0.3751325460760.5656697271840.4313217190580.08461835556550.497808923699-0.329645861313-0.0884586521851-0.1483556861350.2129906868050.01725917330390.06905908536040.145934808016-0.05329673878330.308609693692-23.6638895179-7.53642695638-6.01775319626
21.81330176722-1.14147378004-0.2564633919652.246827928220.5690842090884.035675096270.00222902220269-0.1374342493750.2459951756880.09849004706360.04776214230930.235870354222-0.0786127970129-0.0370209431213-0.04645427563590.106072678578-0.007286388274660.0262425051430.0660532775753-0.02079478200230.187332661596-20.1448413755-11.3793150345-9.81881877896
30.794060451222-0.01556758524250.5447346497762.79680579823-0.20677228622.172447549360.0837527382825-0.04427251367630.541532597509-0.0121415343483-0.001717075045090.198228580225-0.420463112288-0.0409770882826-0.03299218714530.1648722379390.002998526252130.0383520275050.07579606353980.01647038874290.258917383559-21.3507885496-6.73617740702-16.9026991527
41.43979973160.028358786977-0.5668787067191.61279832802-0.5720641929471.934868970150.0177697880379-0.1168889601520.02430206555280.0136415396402-0.0206256142146-0.01777052649510.01514292733680.1399810669910.00642236584440.05252111553720.00382820010678-0.009141289479240.0737316184066-0.00363454674630.0905272208014-16.7007626388-22.8631649323-10.4128058779
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 32 through 64 )32 - 641 - 33
22chain 'A' and (resid 65 through 76 )65 - 7634 - 45
33chain 'A' and (resid 77 through 102 )77 - 10246 - 71
44chain 'A' and (resid 103 through 265 )103 - 26572 - 234

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