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- PDB-7yhc: Crystal structure of VIM-2 MBL in complex with 3-(4-(3-aminopheny... -

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Basic information

Entry
Database: PDB / ID: 7yhc
TitleCrystal structure of VIM-2 MBL in complex with 3-(4-(3-aminophenyl)-1H-1,2,3-triazol-1-yl)phthalic acid
ComponentsBeta-lactamase class B VIM-2
KeywordsHYDROLASE/INHIBITOR / Metallo-beta-lactamase VIM-2 / HYDROLASE / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


hydrolase activity / metal ion binding
Similarity search - Function
: / : / 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-IU3 / Beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.153 Å
AuthorsLi, G.-B. / Yan, Y.-H.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82122065 China
National Natural Science Foundation of China (NSFC)82073698 China
National Natural Science Foundation of China (NSFC)81874291 China
CitationJournal: Eur.J.Med.Chem. / Year: 2023
Title: Metal binding pharmacophore click-derived discovery of new broad-spectrum metallo-beta-lactamase inhibitors.
Authors: Yan, Y.H. / Ding, H.S. / Zhu, K.R. / Mu, B.S. / Zheng, Y. / Huang, M.Y. / Zhou, C. / Li, W.F. / Wang, Z. / Wu, Y. / Li, G.B.
History
DepositionJul 13, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 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

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Assembly

Deposited unit
A: Beta-lactamase class B VIM-2
B: Beta-lactamase class B VIM-2
C: Beta-lactamase class B VIM-2
D: Beta-lactamase class B VIM-2
E: Beta-lactamase class B VIM-2
F: Beta-lactamase class B VIM-2
G: Beta-lactamase class B VIM-2
H: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,07632
Polymers197,4368
Non-polymers3,64124
Water11,764653
1
A: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1354
Polymers24,6791
Non-polymers4553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1354
Polymers24,6791
Non-polymers4553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1354
Polymers24,6791
Non-polymers4553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1354
Polymers24,6791
Non-polymers4553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1354
Polymers24,6791
Non-polymers4553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1354
Polymers24,6791
Non-polymers4553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1354
Polymers24,6791
Non-polymers4553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1354
Polymers24,6791
Non-polymers4553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.240, 246.239, 88.285
Angle α, β, γ (deg.)90.000, 93.950, 90.000
Int Tables number4
Space group name H-MP1211

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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.: 8
Source method: isolated from a genetically manipulated source
Details: Pseudomonas aeruginosa / 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.: 16 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-IU3 / 3-[4-(3-aminophenyl)-1,2,3-triazol-1-yl]phthalic acid


Mass: 324.291 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C16H12N4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 653 / 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: 2.21 Å3/Da / Density % sol: 44.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Magnesium Formate, 23-30% (v/v) Polyethylene glycol 3350

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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 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→19.87 Å / Num. obs: 91180 / % possible obs: 98.95 % / Redundancy: 6.6 % / Biso Wilson estimate: 33.52 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Net I/σ(I): 14.5
Reflection shellResolution: 2.15→2.23 Å / Rmerge(I) obs: 0.346 / Num. unique obs: 8308 / CC1/2: 0.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.35 Å19.83 Å
Translation6.35 Å19.83 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
HKL-2000data scaling
PHASER2.6.0phasing
PHENIX1.10.1refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JN6

6jn6


Resolution: 2.153→19.828 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.74 / Phase error: 23.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2173 1996 2.2 %
Rwork0.1725 88579 -
obs0.1735 90575 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.76 Å2 / Biso mean: 35.6167 Å2 / Biso min: 17.08 Å2
Refinement stepCycle: final / Resolution: 2.153→19.828 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13864 0 208 653 14725
Biso mean--39.58 38.3 -
Num. residues----1848
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0214480
X-RAY DIFFRACTIONf_angle_d0.84119728
X-RAY DIFFRACTIONf_chiral_restr0.0522240
X-RAY DIFFRACTIONf_plane_restr0.0052592
X-RAY DIFFRACTIONf_dihedral_angle_d14.4868320
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.153-2.20660.2781270.245551286
2.2066-2.26610.23761380.20066415100
2.2661-2.33270.27671480.20376389100
2.3327-2.40790.31611440.2036407100
2.4079-2.49380.30291450.20016456100
2.4938-2.59340.23581430.18446351100
2.5934-2.71120.24661490.18546429100
2.7112-2.85370.25111360.1886447100
2.8537-3.03190.24321410.18796367100
3.0319-3.26510.22281460.1768636599
3.2651-3.59190.21691440.161639999
3.5919-4.10770.18191520.1529638299
4.1077-5.16010.16351340.1424636999
5.1601-19.8280.18931490.1707629197

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