[English] 日本語
Yorodumi
- PDB-7dyz: Crystal structure of VIM-2 MBL in complex with 1-(but-3-en-1-yl)-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7dyz
TitleCrystal structure of VIM-2 MBL in complex with 1-(but-3-en-1-yl)-4-methyl-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


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
1-but-3-enyl-4-methyl-imidazole-2-carboxylic acid / beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.902 Å
AuthorsYan, Y.-H. / Li, G.-B.
Funding support China, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)81874291 China
National Science Foundation (NSF, China)81502989 China
National Science Foundation (NSF, China)82073698 China
CitationJournal: Eur.J.Med.Chem. / Year: 2022
Title: Structure-guided optimization of 1H-imidazole-2-carboxylic acid derivatives affording potent VIM-Type metallo-beta-lactamase inhibitors.
Authors: Yan, Y.H. / Li, W. / Chen, W. / Li, C. / Zhu, K.R. / Deng, J. / Dai, Q.Q. / Yang, L.L. / Wang, Z. / Li, G.B.
History
DepositionJan 23, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)25,0835
Polymers24,6791
Non-polymers4034
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-79 kcal/mol
Surface area9350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.864, 45.977, 64.553
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
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
Details: Pseudomonas aeruginosa / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: blaVIM-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9K2N0
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-HQR / 1-but-3-enyl-4-methyl-imidazole-2-carboxylic acid


Mass: 180.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M Magnesium Formate, 23-30% (v/v) Polyethylene glycol 3350

-
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: Jul 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9017→52.63 Å / Num. obs: 19599 / % possible obs: 89.4 % / Redundancy: 11.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.023 / Rrim(I) all: 0.081 / Net I/σ(I): 21.4
Reflection shellResolution: 1.902→1.935 Å / Rmerge(I) obs: 0.735 / Num. unique obs: 590 / CC1/2: 0.755 / Rpim(I) all: 0.276 / Rrim(I) all: 0.788

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
DENZOdata reduction
PDB_EXTRACT3.27data extraction
Aimlessdata scaling
PHASER2.6.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LCA

5lca


Resolution: 1.902→52.625 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2203 1959 10 %
Rwork0.1752 17638 -
obs0.1796 19597 89.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.7 Å2 / Biso mean: 30.8112 Å2 / Biso min: 16.64 Å2
Refinement stepCycle: final / Resolution: 1.902→52.625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1733 0 21 124 1878
Biso mean--31.98 35.18 -
Num. residues----231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141802
X-RAY DIFFRACTIONf_angle_d0.8112451
X-RAY DIFFRACTIONf_chiral_restr0.056280
X-RAY DIFFRACTIONf_plane_restr0.005321
X-RAY DIFFRACTIONf_dihedral_angle_d15.3431042
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.902-1.94930.2952860.210377757
1.9493-2.0020.2382980.199687663
2.002-2.06090.22871090.197697972
2.0609-2.12740.24171040.181694968
2.1274-2.20350.23521500.1757135097
2.2035-2.29170.22331530.1775137199
2.2917-2.3960.21511550.17291398100
2.396-2.52230.20951540.17831388100
2.5223-2.68030.2121570.18031412100
2.6803-2.88730.2211550.18191395100
2.8873-3.17780.22821560.17381409100
3.1778-3.63750.18871590.16491429100
3.6375-4.58250.23081530.155137895
4.5825-52.6250.22281700.18881527100

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more