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- PDB-9cv2: Crystal structure of the metallo-beta-lactamase VIM-20 with D-cap... -

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Basic information

Entry
Database: PDB / ID: 9cv2
TitleCrystal structure of the metallo-beta-lactamase VIM-20 with D-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
Chem-MCO / beta-lactamase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 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)26,2985
Polymers25,8851
Non-polymers4144
Water2,720151
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)67.642, 77.318, 78.854
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-493-

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-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.: 151 / 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: 38.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Magnesium Chloride, 0.1 M 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: 1.00001 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: 1.57→39.43 Å / Num. obs: 78569 / % possible obs: 97.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 17.8 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.025 / Rrim(I) all: 0.058 / Net I/σ(I): 13.13
Reflection shellResolution: 1.57→1.63 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 18.7 / Num. unique obs: 3805 / CC1/2: 0.995 / Rpim(I) all: 0.038 / Rrim(I) all: 0.1 / % possible all: 94.3

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→39.43 Å / SU ML: 0.142 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 18.4081
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1811 2997 5.52 %
Rwork0.1666 51288 -
obs0.1674 51288 97.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.67 Å2
Refinement stepCycle: LAST / Resolution: 1.57→39.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1757 0 17 151 1925
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00641839
X-RAY DIFFRACTIONf_angle_d0.90622518
X-RAY DIFFRACTIONf_chiral_restr0.0823289
X-RAY DIFFRACTIONf_plane_restr0.0326331
X-RAY DIFFRACTIONf_dihedral_angle_d18.1362681
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.60.23151400.19142318X-RAY DIFFRACTION93.18
1.6-1.620.2261470.18432420X-RAY DIFFRACTION95.11
1.62-1.650.19561230.17522431X-RAY DIFFRACTION95.94
1.65-1.680.19861360.172381X-RAY DIFFRACTION96.77
1.68-1.720.21041410.16552473X-RAY DIFFRACTION96.96
1.72-1.760.15591480.16612437X-RAY DIFFRACTION96.93
1.76-1.80.19381320.16772441X-RAY DIFFRACTION97.09
1.8-1.840.17731430.17062446X-RAY DIFFRACTION97.15
1.84-1.890.19711640.1762443X-RAY DIFFRACTION97.53
1.89-1.950.21921370.18362411X-RAY DIFFRACTION97.51
1.95-2.010.22711580.16822445X-RAY DIFFRACTION97.34
2.01-2.080.16511280.1662459X-RAY DIFFRACTION96.6
2.08-2.170.22771500.16972427X-RAY DIFFRACTION97.95
2.17-2.260.18731380.17342472X-RAY DIFFRACTION97.57
2.26-2.380.18891540.17982462X-RAY DIFFRACTION98.42
2.38-2.530.16791330.17542443X-RAY DIFFRACTION97.95
2.53-2.730.19171410.17292486X-RAY DIFFRACTION98.28
2.73-30.21211390.18772463X-RAY DIFFRACTION98.11
3-3.440.17221470.16652472X-RAY DIFFRACTION97.91
3.44-4.330.14881510.14482463X-RAY DIFFRACTION98.12
4.33-39.430.15661470.15022495X-RAY DIFFRACTION99.25
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)
11.84209890457-0.808024727446-0.2597629341893.013433315410.690936235554.065660301510.236104331006-0.2540516861580.6609649507430.4696039988070.001384836690680.429574018866-0.376511255448-0.153677003961-0.1450748107320.2820531836870.01088211284160.0958035699440.182333799654-0.05184681164090.336589703367-23.5711913289-7.52568334341-5.8163322262
21.08373514977-1.17048566331.260221746452.931237006620.593520669613.442420585640.154869926273-0.09508439114740.4990527956750.06451067704340.04417158422190.236797481758-0.239761182302-0.00602076182186-0.1414071424390.12756087333-0.01383959556810.03444259649940.077368649676-0.007645333498020.209291549033-18.841556757-11.0038443977-13.2464003823
32.95711472313-0.186447821376-0.4691663342522.967286915890.07248579411313.588914445350.0764391882524-0.01004586485321.006590855690.1696642749620.2549156542740.507017780801-0.888522001592-0.09969874605560.1194987949690.3118339501340.04184769745580.07839183621430.1069376213820.04019887927520.386067274911-24.3468834068-3.26697710772-16.4208871863
42.51251047755-0.166051170729-0.7520729432944.53606309965-0.5696759079892.330396486890.03150430261960.1485182122240.0141671881951-0.2116578486040.05136381121390.1989780320960.0506928570711-0.100869519008-0.06283403845020.1040500744640.00401020459866-0.01641862760640.1152375599480.02625515760620.118928490246-21.1665799538-18.036017155-21.0174947523
53.2697512545-0.00566957918780.5926300453092.71635111084-0.8365273290163.675809272950.01768931580150.345832158602-0.139528553827-0.299156223332-0.1316409001250.0005083935122750.3549632613510.1534308244580.08958996858220.167885159910.01284080082140.00848499825040.102352556458-0.01220749096280.125997391841-16.626262904-25.0616266515-22.1621315993
61.845715855320.426891452686-1.173984844822.22772366206-0.4885931678862.890347648250.00322814041451-0.1870450997680.04837694913030.0253030908712-0.022527314474-0.06921659033670.09462325470040.2962245447710.009527639070570.08799343767910.0147707176487-0.02749003490210.1240548766030.01153355165330.131161129467-14.8948419212-22.7757140579-8.68972817055
73.385248795291.05701854752-0.6909382417851.378018541660.3851752913951.39300043436-0.306285827002-0.373998811295-1.03126823750.3011850579580.082289350566-0.9812317826290.8454559506171.10291858314-0.1767826403470.08103263231280.171881788984-0.08545507775740.2945264922580.1407524724330.154402722312-10.8510020945-30.2998258812-3.81043222021
83.06350919641-0.232836559939-0.410158439411.93935209051-0.394559083491.029745574550.18966128407-0.4784901876570.4900761240550.401062022469-0.152106714194-0.262378567885-0.25235412410.869455730310.01640247587410.165370733014-0.0836915229542-0.02456991832560.358726066928-0.05395651944150.216925535355-11.8390117243-16.4557471781-2.0533161563
95.758052364332.982932285210.4126822203267.63846756421-0.4199924046264.623750405170.208596357356-0.455913186251-0.3175370364880.351804169217-0.242669390206-0.06608332312650.2252757224820.1069934114060.06111762202070.1558008550560.0192489583394-0.001107909747060.1525029470050.02316102238030.0749195331322-19.9028050298-30.14845952673.92560180883
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 88 )65 - 8834 - 57
33chain 'A' and (resid 89 through 102 )89 - 10258 - 71
44chain 'A' and (resid 103 through 146 )103 - 14672 - 115
55chain 'A' and (resid 147 through 162 )147 - 162116 - 131
66chain 'A' and (resid 163 through 215 )163 - 215132 - 184
77chain 'A' and (resid 216 through 229 )216 - 229185 - 198
88chain 'A' and (resid 230 through 245 )230 - 245199 - 214
99chain 'A' and (resid 246 through 264 )246 - 264215 - 233

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