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- PDB-5n5h: Crystal structure of metallo-beta-lactamase VIM-1 in complex with... -

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Basic information

Entry
Database: PDB / ID: 5n5h
TitleCrystal structure of metallo-beta-lactamase VIM-1 in complex with ML302F inhibitor
ComponentsBeta-lactamase VIM-1
KeywordsHYDROLASE / lactamase / inhibitor / carbapenemase
Function / homology
Function and homology information


: / : / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-S3C / Beta-lactamase VIM-1
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsSalimraj, R. / Hinchliffe, P. / Spencer, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/N002679/1 United Kingdom
CitationJournal: FEBS J. / Year: 2019
Title: Crystal structures of VIM-1 complexes explain active site heterogeneity in VIM-class metallo-beta-lactamases.
Authors: Salimraj, R. / Hinchliffe, P. / Kosmopoulou, M. / Tyrrell, J.M. / Brem, J. / van Berkel, S.S. / Verma, A. / Owens, R.J. / McDonough, M.A. / Walsh, T.R. / Schofield, C.J. / Spencer, J.
History
DepositionFeb 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase VIM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3134
Polymers26,8991
Non-polymers4143
Water4,270237
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.684, 67.652, 40.217
Angle α, β, γ (deg.)90.00, 91.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase VIM-1 / Class B carbapenemase VIM-1 / Metallo-beta-lactamase / Metallo-beta-lactamase VIM-1 / Metallobeta- ...Class B carbapenemase VIM-1 / Metallo-beta-lactamase / Metallo-beta-lactamase VIM-1 / Metallobeta-lactamase / VIM-1 / VIM-1 metallo-beta lactamase / VIM-1 metallo-beta-lactamase / VIM-1 protein


Mass: 26898.760 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: blaVIM, blaVIM-1 / Plasmid: pOPINE / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: Q9XAY4
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-S3C / (2Z)-2-sulfanyl-3-(2,3,6-trichlorophenyl)prop-2-enoic acid


Mass: 283.559 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H5Cl3O2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O

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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: 38.7 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.02 M Na-formate, 0.02 M NH4-acetate, 0.02 M Na3-citrate, 0.02 M NaK-tartrate, 0.02 M Na-oxamate, 0.1 M Morpheus (42) Buffer 1 pH 6.5, 12.5% w/v PEG 3350, 12.5% w/v PEG 1000 and 12.5% w/v MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.3→28.582 Å / Num. obs: 52058 / % possible obs: 99.8 % / Redundancy: 6.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.077 / Net I/σ(I): 21.5
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 7.9 / CC1/2: 0.881 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N5G

5n5g


Resolution: 1.3→28.582 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 16.7
RfactorNum. reflection% reflection
Rfree0.1678 2684 5.16 %
Rwork0.1545 --
obs0.1552 52032 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.3→28.582 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1749 0 17 237 2003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.021838
X-RAY DIFFRACTIONf_angle_d1.6752523
X-RAY DIFFRACTIONf_dihedral_angle_d14.092655
X-RAY DIFFRACTIONf_chiral_restr0.103287
X-RAY DIFFRACTIONf_plane_restr0.01334
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.32360.30861270.29162579X-RAY DIFFRACTION99
1.3236-1.34910.28861190.26812585X-RAY DIFFRACTION99
1.3491-1.37660.2971290.24932585X-RAY DIFFRACTION99
1.3766-1.40660.22421450.21482583X-RAY DIFFRACTION100
1.4066-1.43930.20161610.19612566X-RAY DIFFRACTION100
1.4393-1.47530.20521220.18412618X-RAY DIFFRACTION100
1.4753-1.51520.17751410.1712586X-RAY DIFFRACTION100
1.5152-1.55970.17181420.16442593X-RAY DIFFRACTION100
1.5597-1.61010.17391360.16372615X-RAY DIFFRACTION100
1.6101-1.66760.14821450.16232606X-RAY DIFFRACTION100
1.6676-1.73440.16921560.15472584X-RAY DIFFRACTION100
1.7344-1.81330.15741410.14552592X-RAY DIFFRACTION100
1.8133-1.90890.16141670.14452583X-RAY DIFFRACTION100
1.9089-2.02850.13411620.13762564X-RAY DIFFRACTION100
2.0285-2.1850.13921370.12842614X-RAY DIFFRACTION100
2.185-2.40480.15811460.13232596X-RAY DIFFRACTION100
2.4048-2.75260.16721200.13652635X-RAY DIFFRACTION100
2.7526-3.4670.15791480.14152599X-RAY DIFFRACTION99
3.467-28.5820.14971400.13442665X-RAY DIFFRACTION99
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)
12.48360.6888-0.62391.8651-0.67352.1272-0.10650.149-0.4442-0.2505-0.0686-0.38250.34280.21890.12890.10640.02860.0490.15290.02860.2045-3.9442-10.5482-9.0139
22.4381.8464-0.12124.5362-0.12261.81410.01-0.0659-0.0615-0.0487-0.0955-0.08120.1333-0.02130.03950.03020.00940.00770.05820.00750.0521-11.2707-9.7029-5.1462
30.8285-1.16030.04662.51760.64273.5034-0.0946-0.0982-0.01670.06110.0709-0.1855-0.06470.2563-0.00760.02820.00520.00270.07780.0110.0621-10.6296-3.22722.0328
46.4162.5664-0.1134.60720.30852.22520.0277-0.0801-0.0683-0.0433-0.0969-0.37070.09590.3230.06640.05350.02990.00780.10740.04180.1112-3.9938-10.60593.531
51.4564-0.15430.00641.2394-0.18761.0401-0.014-0.06060.02510.0342-0.0136-0.08260.04690.11840.02190.03990.00760.00650.07210.00460.0526-15.1745-5.04152.1056
63.04560.04390.82912.9545-0.57262.18090.0182-0.1239-0.07150.23820.01560.1550.07710.0013-0.01280.08310.00650.02930.0602-0.00540.0362-22.3699-5.63547.634
71.219-0.56270.74452.5681-2.23942.8892-0.0718-0.03140.02660.07770.0280.1512-0.0718-0.1690.03830.07660.01340.01640.0799-0.01620.0761-25.69660.49733.5493
81.87980.4171.44431.77931.04312.7077-0.0974-0.07320.1601-0.04190.01860.1361-0.1401-0.10880.05050.03730.01210.01140.0482-0.00520.0523-22.8763.6222-4.3066
91.899-0.0832-0.10141.6544-0.18432.2144-0.00590.0932-0.0459-0.11740.00540.07930.1173-0.0851-0.00650.0650.00840.00890.06610.01360.0573-19.4444-3.3582-11.8322
103.8170.72390.28095.6795-1.08952.2589-0.06280.19980.2823-0.33240.13820.344-0.0761-0.2163-0.05310.0780.0099-0.00930.10.01240.066-27.67072.5698-15.5453
112.2211-0.8926-0.01643.944-0.17591.93010.07030.17270.2588-0.2255-0.0525-0.2618-0.13120.15340.0180.0738-0.00160.01660.07180.01480.0772-13.41020.7524-14.5875
123.6862.87040.90313.26560.29461.5070.06110.2553-0.0896-0.087-0.07810.26380.1405-0.318-0.010.1049-0.0151-0.0040.1449-0.01840.1085-26.1489-6.4471-21.7386
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 52 )
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 76 )
3X-RAY DIFFRACTION3chain 'A' and (resid 77 through 88 )
4X-RAY DIFFRACTION4chain 'A' and (resid 89 through 102 )
5X-RAY DIFFRACTION5chain 'A' and (resid 103 through 122 )
6X-RAY DIFFRACTION6chain 'A' and (resid 123 through 146 )
7X-RAY DIFFRACTION7chain 'A' and (resid 147 through 163 )
8X-RAY DIFFRACTION8chain 'A' and (resid 164 through 183 )
9X-RAY DIFFRACTION9chain 'A' and (resid 184 through 215 )
10X-RAY DIFFRACTION10chain 'A' and (resid 216 through 229 )
11X-RAY DIFFRACTION11chain 'A' and (resid 230 through 245 )
12X-RAY DIFFRACTION12chain 'A' and (resid 246 through 264 )

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