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- PDB-7chv: Metallo-Beta-Lactamase VIM-2 in complex with 1-benzyl-1H-imidazol... -

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Basic information

Entry
Database: PDB / ID: 7chv
TitleMetallo-Beta-Lactamase VIM-2 in complex with 1-benzyl-1H-imidazole-2-carboxylic acid
ComponentsBeta-lactamase class B VIM-2
KeywordsHYDROLASE / Metallo-beta-lactamase VIM-2 / VIM-2
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
FORMIC ACID / 1-(phenylmethyl)imidazole-2-carboxylic acid / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.174 Å
AuthorsYan, Y.-H. / Li, G.-B.
Funding support China, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)81874291 China
National Science Foundation (NSF, China)81502989 China
CitationJournal: Acta Pharm Sin B / Year: 2021
Title: AncPhore: A versatile tool for anchor pharmacophore steered drug discovery with applications in discovery of new inhibitors targeting metallo-beta-lactamases and indoleamine/tryptophan 2,3-dioxygenases.
Authors: Dai, Q. / Yan, Y. / Ning, X. / Li, G. / Yu, J. / Deng, J. / Yang, L. / Li, G.B.
History
DepositionJul 6, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1707
Polymers24,6791
Non-polymers4906
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-80 kcal/mol
Surface area9620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.655, 78.891, 79.808
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Beta-lactamase class B VIM-2 / BlaVIM-2 / Metallo beta lactamase VIM-2 / Metallo beta-lactamase / Metallo-beta lactamase protein / ...BlaVIM-2 / Metallo beta lactamase VIM-2 / Metallo beta-lactamase / Metallo-beta lactamase protein / Metallo-beta-lactamase VIM-2 / VIM-2 class B beta-lactamase / VIM-2 class B metallo b-lactamase / VIM-2 metallo beta-lactamase / VIM-2 type metallo-beta-lactamase


Mass: 24679.439 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: blaVIM-2, bla vim-2, bla-VIM-2, blasVIM-2, blaVIM2, blm, VIM-2, vim-2, PAERUG_P32_London_17_VIM_2_10_11_06255
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9K2N0
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-FZX / 1-(phenylmethyl)imidazole-2-carboxylic acid


Mass: 202.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H10N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.19 Å3/Da / Density % sol: 43.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 28%-35%PEG3350, 0.1M Mg(COOH)2

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Data collection

DiffractionMean temperature: 195 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 X CdTe 1M / Detector: PIXEL / Date: May 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.17→50 Å / Num. obs: 11610 / % possible obs: 99.9 % / Redundancy: 10 % / Biso Wilson estimate: 41.04 Å2 / Rmerge(I) obs: 0.226 / Rpim(I) all: 0.078 / Rrim(I) all: 0.24 / Χ2: 2.163 / Net I/σ(I): 3.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.248.21.0015690.5640.3641.0670.86399.8
2.24-2.289.71.0045720.6920.3381.0610.783100
2.28-2.3210.10.9295620.7210.3050.9790.843100
2.32-2.3710.20.7965890.7950.2590.8380.948100
2.37-2.4210.50.7115540.7750.230.7481.155100
2.42-2.4810.40.6725750.810.2180.7071.219100
2.48-2.5410.40.6065700.8130.1960.6381.414100
2.54-2.6110.60.5545620.8460.1790.5821.453100
2.61-2.6910.30.4985910.8810.1630.5251.767100
2.69-2.7710.10.465810.9050.1510.4852.04999.7
2.77-2.8790.3855710.9320.1350.4092.23999.8
2.87-2.9910.40.3485730.9480.1140.3672.252100
2.99-3.1210.80.3135720.9630.1010.3292.472100
3.12-3.2910.70.2655860.9540.0870.2792.816100
3.29-3.4910.30.2385830.9630.080.2513.381100
3.49-3.76100.25800.9660.0680.2113.366100
3.76-4.149.10.1795880.9770.0650.1913.49499.7
4.14-4.749.80.1595980.9730.0560.1693.59899.8
4.74-5.9710.20.1525960.9870.0510.1613.11799.7
5.97-509.10.1466380.8950.0560.1573.7899.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.98 Å39.45 Å
Translation5.98 Å39.45 Å

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASER2.6.0phasing
PHENIX1.10.1-2155refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JN6

6jn6


Resolution: 2.174→34.327 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 38.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3635 1160 10 %
Rwork0.2453 10442 -
obs0.2566 11602 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.53 Å2 / Biso mean: 44.1638 Å2 / Biso min: 16.33 Å2
Refinement stepCycle: final / Resolution: 2.174→34.327 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1720 0 24 31 1775
Biso mean--43.34 37.91 -
Num. residues----231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0211793
X-RAY DIFFRACTIONf_angle_d1.2762435
X-RAY DIFFRACTIONf_chiral_restr0.06279
X-RAY DIFFRACTIONf_plane_restr0.008319
X-RAY DIFFRACTIONf_dihedral_angle_d15.6291030
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.174-2.27270.42221340.3286119492
2.2727-2.39250.41321410.33141293100
2.3925-2.54230.40511450.31121310100
2.5423-2.73850.38441460.29481296100
2.7385-3.0140.42031450.28061309100
3.014-3.44980.42421490.27131320100
3.4498-4.3450.35181470.21981333100
4.345-34.3270.28991530.1914138799

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