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- PDB-9cv3: Crystal structure of the metallo-beta-lactamase VIM-20 with L-cap... -

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Basic information

Entry
Database: PDB / ID: 9cv3
TitleCrystal structure of the metallo-beta-lactamase VIM-20 with L-captopril
ComponentsMetallo-beta-lactamase VIM-20
KeywordsHYDROLASE / metallo-beta-lactamase
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / periplasmic space / hydrolase activity / response to antibiotic / metal ion binding
Similarity search - Function
: / : / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
ACETATE ION / L-CAPTOPRIL / beta-lactamase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 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 9, 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 VIM-20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4758
Polymers25,8851
Non-polymers5917
Water3,639202
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)67.845, 77.595, 79.052
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-471-

HOH

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Components

#1: Protein Metallo-beta-lactamase VIM-20


Mass: 25884.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: blaVIM-20 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A344X7M2
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#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: medication*YM
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.1 Å3/Da / Density % sol: 41.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Ammonium Acetate, 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: 1.000034 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000034 Å / Relative weight: 1
ReflectionResolution: 1.51→38.8 Å / Num. obs: 126069 / % possible obs: 99.42 % / Redundancy: 6.9 % / Biso Wilson estimate: 11.52 Å2 / CC1/2: 0.918 / Net I/σ(I): 17.1
Reflection shellResolution: 1.51→1.56 Å / Redundancy: 6.19 % / Mean I/σ(I) obs: 3 / Num. unique obs: 2037 / CC1/2: 0.683 / % possible all: 99.65

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→38.8 Å / SU ML: 0.1518 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.9806
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2117 1500 4.53 %
Rwork0.1923 60214 -
obs0.1932 33065 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.19 Å2
Refinement stepCycle: LAST / Resolution: 1.51→38.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1749 0 29 202 1980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00891829
X-RAY DIFFRACTIONf_angle_d1.14792503
X-RAY DIFFRACTIONf_chiral_restr0.09286
X-RAY DIFFRACTIONf_plane_restr0.0066332
X-RAY DIFFRACTIONf_dihedral_angle_d15.1822659
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.530.29531350.2572862X-RAY DIFFRACTION99.6
1.53-1.560.25311300.24522832X-RAY DIFFRACTION99.66
1.56-1.590.29311370.24762904X-RAY DIFFRACTION99.84
1.59-1.620.26881480.24392870X-RAY DIFFRACTION99.9
1.62-1.650.25511350.23582890X-RAY DIFFRACTION99.7
1.65-1.690.22411250.2162838X-RAY DIFFRACTION99.8
1.69-1.730.22491520.20052868X-RAY DIFFRACTION99.83
1.73-1.770.20941280.20062862X-RAY DIFFRACTION99.73
1.77-1.820.21231360.19472896X-RAY DIFFRACTION99.8
1.82-1.870.23281290.19522883X-RAY DIFFRACTION99.8
1.87-1.930.16561380.19512859X-RAY DIFFRACTION99.83
1.93-20.21111410.20352855X-RAY DIFFRACTION99.87
2-2.080.21851440.18212871X-RAY DIFFRACTION99.74
2.08-2.180.25051400.19022884X-RAY DIFFRACTION99.51
2.18-2.290.23161350.18592828X-RAY DIFFRACTION99.26
2.29-2.440.2191310.19962872X-RAY DIFFRACTION99.73
2.44-2.620.19891420.18572878X-RAY DIFFRACTION99.9
2.62-2.890.21571350.19142863X-RAY DIFFRACTION99.54
2.89-3.310.21511390.18632881X-RAY DIFFRACTION99.8
3.31-4.160.16131360.16352860X-RAY DIFFRACTION99.47
4.16-38.80.18531400.17122858X-RAY DIFFRACTION98.75
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)
12.26965152344-0.79225910013-0.02532802680840.5383220543551.040577500344.25498062861-0.363884148119-0.3681356517-0.7227687670660.502330112441-0.0085577184377-0.512554824810.5675644633130.778625465510.3485524414620.2858522739340.0663957511772-9.16876165432E-50.2016075231850.1024077609190.386692858713-7.17330790455-33.5380175897-3.64621697478
25.849539659181.891897568531.245367999292.987129851540.1947667711462.101952962670.030613998565-0.245128635124-0.3010630822980.1722160018790.0857525472185-0.1784301620320.0259405483294-0.0551396036753-0.1190583983630.129193106664-0.0150645845916-0.02493952511140.1280655386720.04068685795410.133274820051-12.4130132718-29.9122034639-7.39540596992
31.25767124785-0.41041060246-0.2169676812312.043415356370.01965374265562.138236527080.122440839053-0.0553757666414-0.273675583387-0.0177992023976-0.0841621227226-0.1210750256740.0585592746307-0.0361297282308-0.04281386435670.0635079765903-0.00342151214688-0.01732675796930.0517052600543-0.005441252847020.087654755833-15.1574460768-27.6844584629-13.2892650003
41.547947887740.02479661239040.1516075059122.940016744950.3623349342481.08927241050.0471712879390.052127464174-0.151945169828-0.03709131473050.0115823880494-0.1664442601070.08673419690080.0153410972728-0.05217934293060.06355011031040.008239243547620.004832025909590.096851102984-0.02339898466380.0609213966462-12.0612787582-24.0202965563-19.9277364135
50.7994133101910.11508163444-0.9360128290241.528141986771.078822077762.077100970890.03781494534790.256980913642-0.0108564177365-0.29672075707-0.1227657847030.00340994140789-0.268305880981-0.1308965607610.07348227345990.1046224781590.00875516637069-0.005548577879080.061436274436-0.004033832098830.0576644080136-17.1664657583-13.56077399-22.182620814
60.6847936498220.2193525912430.3182861404681.535602192210.2689833164911.50876518013-0.0117199377328-0.119390162936-0.02066410685990.0259212763558-0.02601832693220.0610980388579-0.0684943832018-0.1827391451790.02934298051780.06641694754260.005747992217270.01717429530380.11466922856-0.005256052653610.0512985174501-19.756308429-13.8959708764-7.56832111345
70.954948683101-0.505317163647-0.1492640284951.28169416931-0.001873408917071.898325427830.0553368432313-0.0957449496932-0.07521914777870.121854649924-0.0258458906838-0.00437505718329-0.0273387756871-0.272597067537-0.002743976646730.0703027120548-0.009176899699470.003060759682410.1240132669130.01329291159320.0376802383285-17.9499089598-14.86868827281.3591516886
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 44 )32 - 441 - 13
22chain 'A' and (resid 45 through 64 )45 - 6414 - 33
33chain 'A' and (resid 65 through 88 )65 - 8834 - 57
44chain 'A' and (resid 89 through 146 )89 - 14658 - 115
55chain 'A' and (resid 147 through 162 )147 - 162116 - 131
66chain 'A' and (resid 163 through 229 )163 - 229132 - 198
77chain 'A' and (resid 230 through 263 )230 - 263199 - 232

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