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- PDB-9cv5: Crystal structure of the metallo-beta-lactamase VIM-31 with L-cap... -

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Basic information

Entry
Database: PDB / ID: 9cv5
TitleCrystal structure of the metallo-beta-lactamase VIM-31 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 / metal ion binding / L-CAPTOPRIL / VIM-31
Function and homology information
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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)26,2325
Polymers25,8601
Non-polymers3724
Water2,846158
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, 77.222, 79.036
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-542-

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.: 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.: 158 / 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: 38.31 %
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: 1.4→39.52 Å / Num. obs: 75546 / % possible obs: 96.02 % / Redundancy: 3.1 % / Biso Wilson estimate: 16.59 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.02222 / Rpim(I) all: 0.01396 / Rrim(I) all: 0.02633 / Net I/σ(I): 24.24
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.2027 / Num. unique obs: 1682 / CC1/2: 0.911 / Rpim(I) all: 0.2021 / Rrim(I) all: 0.2862 / % possible all: 58.08

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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: 1.4→39.52 Å / SU ML: 0.1192 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.4516
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1836 3745 4.96 %
Rwork0.1588 71798 -
obs0.16 75543 96.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.03 Å2
Refinement stepCycle: LAST / Resolution: 1.4→39.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1730 0 17 158 1905
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00621788
X-RAY DIFFRACTIONf_angle_d0.91142451
X-RAY DIFFRACTIONf_chiral_restr0.0847283
X-RAY DIFFRACTIONf_plane_restr0.0065324
X-RAY DIFFRACTIONf_dihedral_angle_d14.155621
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.2373740.21641608X-RAY DIFFRACTION58.08
1.42-1.440.21211070.19891983X-RAY DIFFRACTION71.19
1.44-1.460.20991360.17382343X-RAY DIFFRACTION85.72
1.46-1.480.13651190.17542524X-RAY DIFFRACTION90.79
1.48-1.50.20241530.17192640X-RAY DIFFRACTION95.19
1.5-1.520.21581320.16412705X-RAY DIFFRACTION98.88
1.52-1.550.18061460.15742783X-RAY DIFFRACTION99.63
1.55-1.570.19151660.17112764X-RAY DIFFRACTION99.49
1.57-1.60.18251290.16292745X-RAY DIFFRACTION99.72
1.6-1.630.19051450.16362735X-RAY DIFFRACTION99.86
1.63-1.670.19571280.14722811X-RAY DIFFRACTION99.9
1.67-1.70.17031550.15152759X-RAY DIFFRACTION99.9
1.7-1.740.1591470.15122768X-RAY DIFFRACTION99.93
1.74-1.790.18111440.15492753X-RAY DIFFRACTION99.86
1.79-1.830.20621480.16072771X-RAY DIFFRACTION99.73
1.83-1.890.17421470.16082756X-RAY DIFFRACTION99.83
1.89-1.950.18271300.16852751X-RAY DIFFRACTION99.86
1.95-2.020.18361500.15962815X-RAY DIFFRACTION99.83
2.02-2.10.17361470.15752704X-RAY DIFFRACTION99.27
2.1-2.20.17351410.16082770X-RAY DIFFRACTION99.39
2.2-2.310.17481500.16582786X-RAY DIFFRACTION99.73
2.31-2.460.19881410.16742721X-RAY DIFFRACTION99.76
2.46-2.650.24931320.16712784X-RAY DIFFRACTION99.66
2.65-2.910.16821490.17172752X-RAY DIFFRACTION99.69
2.91-3.330.20031410.16692743X-RAY DIFFRACTION99.24
3.33-4.20.15841430.14092738X-RAY DIFFRACTION98.8
4.2-39.520.17671450.14432786X-RAY DIFFRACTION99.66
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)
10.3882784419340.6049059285560.3547676316570.9306989816150.6076863785294.17460048611-0.0317136176825-0.4489844797140.7411197343980.731145115747-0.2100069598180.571109627305-0.110367193073-1.352291417490.2918691063760.3951495043020.02764895975840.04471024451280.300847441973-0.1313159380430.295989072391-27.096094788-5.89515733458-3.38419490575
22.69478231728-0.237534422865-1.349234399312.03493563150.3477021388224.026526607710.124828833912-0.2189175546870.3905230001320.07993640575070.0340092526419-0.0175069006153-0.356096975020.212580812061-0.08506798204860.167911335011-0.02062437876090.03048165147830.114734064151-0.01850061303040.175412287805-20.216286773-10.0709807027-10.5162037162
33.890518980193.153032374020.5109522303556.714077254761.981232303881.66580182471-0.180640801025-0.1133220093320.512498212406-0.2249297039660.108686417580.270138880444-0.7305132820840.0108256378321-0.0238760071780.3663204862090.02197581668810.03567584911930.1569340596080.02774975699290.277686359481-24.1353685433-3.22606557813-16.3087935861
41.33284283657-0.684703540749-0.1267122506752.348397836040.06079175736662.465875111260.1208843855030.07189504967470.267704266576-0.07429822150410.0205769474207-0.0335501441705-0.2167870896850.0896687427235-0.09350955620890.121989021783-0.00298469287190.01628404951620.09646995268160.01514402063950.120902771914-20.0346368159-14.9580929843-17.7349943682
52.455779998210.20513672845-1.005675335765.04979190942-1.329180302312.855170193990.06703976412560.256288554538-0.0814333498217-0.3449074582190.008265955110240.184538795670.121366064423-0.0531298599933-0.0845328165340.1721912225580.0075736238192-0.02637377463870.163446434999-0.01206774729240.110285059439-22.2609420882-20.6526063956-23.9026689769
63.26904825598-1.180799064861.121194858872.62904120917-0.9784073946564.010443527030.10319487810.192674713032-0.109724060208-0.262281997337-0.103164821344-0.04224449819550.2151707015290.2364963156450.0001149123729340.1732407444760.0282399646793-0.0006359789233060.140411931432-0.02882639017190.123187335011-16.6276461816-25.0475929773-22.2843580267
71.52343717326-0.100398032035-0.7596212775221.588257020730.06090673452992.785592418760.0430759742997-0.1814379847010.07301974310520.04845689170740.0306070880235-0.09732651914740.124198265610.376234421378-0.06199103968230.1154788746810.0203960032842-0.02590231097350.151934028452-0.002747688098060.112797871739-14.7984449832-22.7933418674-8.94699068346
83.22753423842-1.298026725310.4872156716350.850889204151-0.05766129346641.3149167925-0.0507212743326-0.275424257165-0.5309883165810.324154000310.0314773681875-0.2508037250210.6471707797170.536399989685-0.002170583099370.2240442437420.101331054687-0.04019699444570.290190012560.02410776225170.155868681726-11.1378914347-30.7002305356-4.23011338476
90.949951899039-0.980617668969-0.4604486784761.47610434372-0.1395935472783.521795425530.00172968432811-0.2899744101170.09457680620690.2354791932340.0647998296436-0.1376322418270.1541027449410.512349944864-0.09191636545560.1486950486840.0127590171876-0.02786541424880.237203100602-0.01512369256360.118330818915-15.5356755973-23.09377529560.823559057212
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 88 )45 - 8814 - 57
33chain 'A' and (resid 89 through 102 )89 - 10258 - 71
44chain 'A' and (resid 103 through 122 )103 - 12272 - 91
55chain 'A' and (resid 123 through 146 )123 - 14692 - 115
66chain 'A' and (resid 147 through 162 )147 - 162116 - 131
77chain 'A' and (resid 163 through 215 )163 - 215132 - 184
88chain 'A' and (resid 216 through 229 )216 - 229185 - 198
99chain 'A' and (resid 230 through 262 )230 - 262199 - 231

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