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- PDB-7ayj: Metallo beta-lactamse Vim-1 with a sulfamoyl inhibitor. -

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Basic information

Entry
Database: PDB / ID: 7ayj
TitleMetallo beta-lactamse Vim-1 with a sulfamoyl inhibitor.
ComponentsBeta-lactamase VIM-1
KeywordsHYDROLASE / VIM1 / metallo beta lactamse / inhibition
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / hydrolase activity / 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-S9N / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsFarley, A.J.M. / Ermolovich, I. / Calvopina, K. / Rabe, P. / Brem, J. / Schofield, C.J.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trust099141/Z/12/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S50676X/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/N002679/1 United Kingdom
CitationJournal: Acs Infect Dis. / Year: 2021
Title: Structural Basis of Metallo-beta-lactamase Inhibition by N -Sulfamoylpyrrole-2-carboxylates.
Authors: Farley, A.J.M. / Ermolovich, Y. / Calvopina, K. / Rabe, P. / Panduwawala, T. / Brem, J. / Bjorkling, F. / Schofield, C.J.
History
DepositionNov 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jun 2, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jun 23, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 31, 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)27,3464
Polymers26,9311
Non-polymers4153
Water4,864270
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)39.533, 67.430, 40.267
Angle α, β, γ (deg.)90.000, 93.510, 90.000
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 / Subclass B1 metallo-beta-lactamase VIM-1 / VIM-1 / VIM-1 metallo-beta-lactamase / VIM-1 protein


Mass: 26930.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: blaVIM, blaVIM-1, CAZ10_38240, CAZ10_38245 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9XAY4
#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-S9N / 3-(4-fluorophenyl)-1-sulfamoyl-pyrrole-2-carboxylic acid


Mass: 284.264 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H9FN2O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 38.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris pH 8.5, 2.4 M ammonium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.21→40.19 Å / Num. obs: 64128 / % possible obs: 99.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 12.678 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.021 / Rrim(I) all: 0.053 / Net I/σ(I): 16.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.21-1.235.60.6282.230740.7210.2980.69995.9
3.28-40.216.446.832950.0140.035100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
xia2data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N5G

5n5g


Resolution: 1.21→40.19 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.24 / Stereochemistry target values: ML
Details: The Zn coordinating Cys is partially oxidized (25 %). The model contains Cys as well as it's oxidized analogue 3-sulfinoalanine (CSD) in a ratio Cys:CSD 0.75:0.25 summing the occupancy to 1.000.
RfactorNum. reflection% reflection
Rfree0.1951 3065 4.79 %
Rwork0.1697 60971 -
obs0.1708 64036 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.38 Å2 / Biso mean: 21.2749 Å2 / Biso min: 8.98 Å2
Refinement stepCycle: final / Resolution: 1.21→40.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1708 0 30 282 2020
Biso mean--24.23 29.78 -
Num. residues----231
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.21-1.230.26511270.25822608273594
1.23-1.250.27431480.24632743289199
1.25-1.270.21821190.228727932912100
1.27-1.290.25651670.238227502917100
1.29-1.320.29761530.237927462899100
1.32-1.350.27341220.236927982920100
1.35-1.370.24261430.213827692912100
1.37-1.410.21831170.227892906100
1.41-1.440.20541400.193227902930100
1.44-1.480.20671610.18327372898100
1.48-1.520.19821480.179927532901100
1.52-1.570.21581420.180527882930100
1.57-1.630.19231260.1727702896100
1.63-1.690.2091170.168127932910100
1.69-1.770.19671700.160227582928100
1.77-1.870.17531470.167727592906100
1.87-1.980.1791460.167327892935100
1.98-2.140.18691360.156327862922100
2.14-2.350.19731650.175627572922100
2.35-2.690.20491330.160328042937100
2.69-3.390.20511350.161528092944100
3.39-40.190.14851030.151128822985100
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)
12.134-0.2607-0.42673.6281-0.23883.6246-0.09140.1266-0.3279-0.2922-0.0758-0.55380.49760.23020.13510.17060.01660.06260.1273-0.01320.259714.7999-10.477911.8638
22.95421.55690.18077.46010.80932.723-0.0126-0.0278-0.0706-0.1519-0.0005-0.10150.1742-0.05770.00910.0737-0.00640.00940.0818-0.00190.07117.4417-7.866215.2989
32.8608-0.6106-0.3841.4407-0.10381.5245-0.0749-0.2403-0.02310.07850.0723-0.11520.06830.09980.00210.0986-0.001-0.00550.1009-0.00870.09386.3623-4.458724.4074
45.8288-0.55681.216.4836-1.48854.72080.026-0.1328-0.08970.01730.04190.29930.2066-0.2351-0.0690.0918-0.00730.03540.1185-0.00620.0844-8.0769-4.502225.9642
55.4897-1.82521.14622.5672-0.00824.8760.0051-0.00850.3613-0.09670.0082-0.0065-0.272-0.27650.01180.14160.0282-0.00010.0963-0.01670.1567-5.11399.341117.5839
62.7929-0.7277-0.32191.6920.24042.5895-0.00350.29340.0018-0.2028-0.04390.0710.0483-0.31560.03710.1242-0.0237-0.00830.15240.00410.0852-2.06460.0527.2255
77.83560.66391.97521.9286-0.3764.3415-0.15210.6844-0.308-0.18760.0360.2220.3399-0.76630.06330.2036-0.0860.02810.3269-0.04380.1476-4.9477-3.3755-1.6645
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 52 )A31 - 52
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 76 )A53 - 76
3X-RAY DIFFRACTION3chain 'A' and (resid 77 through 137 )A77 - 137
4X-RAY DIFFRACTION4chain 'A' and (resid 138 through 155 )A138 - 155
5X-RAY DIFFRACTION5chain 'A' and (resid 156 through 174 )A156 - 174
6X-RAY DIFFRACTION6chain 'A' and (resid 175 through 245 )A175 - 245
7X-RAY DIFFRACTION7chain 'A' and (resid 246 through 262 )A246 - 262

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