[English] 日本語
Yorodumi
- PDB-7cjl: Metallo-Beta-Lactamase VIM-2 in complex with (S)-N-(3-(2H-tetrazo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7cjl
TitleMetallo-Beta-Lactamase VIM-2 in complex with (S)-N-(3-(2H-tetrazol-5-yl)phenyl)-3-mercapto-2-methylpropanamide
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 / Chem-G0O / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.789 Å
AuthorsYan, Y.-H. / Chen, J. / Zhan, Z. / Yu, Z.-J. / Li, G. / Li, G.-B. / Guo, L. / Wu, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81874291 China
National Natural Science Foundation of China (NSFC)81502989 China
CitationJournal: Rsc Adv / Year: 2020
Title: Discovery of mercaptopropanamide-substituted aryl tetrazoles as new broad-spectrum metallo-beta-lactamase inhibitors.
Authors: Yan, Y.H. / Chen, J. / Zhan, Z. / Yu, Z.J. / Li, G. / Guo, L. / Li, G.B. / Wu, Y. / Zheng, Y.
History
DepositionJul 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 3, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)50,1939
Polymers49,3592
Non-polymers8347
Water4,504250
1
B: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1205
Polymers24,6791
Non-polymers4404
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-0 kcal/mol
Surface area9300 Å2
MethodPISA
2
A: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0744
Polymers24,6791
Non-polymers3943
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.356, 90.132, 125.849
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
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.: 2
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.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-G0O / (S)-N-(3-(2H-tetrazol-5-yl)phenyl)-3-mercapto-2-methylpropanamide


Mass: 263.319 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H13N5OS / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.61 Å3/Da / Density % sol: 52.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 28%-32% PEG3350, 0.1M Mg(COOH)2

-
Data collection

DiffractionMean temperature: 195 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X CdTe 1M / Detector: PIXEL / Date: Jul 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 50198 / % possible obs: 99.9 % / Redundancy: 10.6 % / Biso Wilson estimate: 20.14 Å2 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.048 / Rrim(I) all: 0.165 / Χ2: 0.904 / Net I/σ(I): 6.1 / Num. measured all: 533790
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.78-1.845.51.77948990.3320.7921.960.63599.2
1.84-1.928.21.63549440.5290.5941.7430.695100
1.92-29.91.26249470.7820.4161.3310.75899.9
2-2.1110.40.8749630.8770.280.9160.875100
2.11-2.2411.90.65949980.9320.1970.6891.08100
2.24-2.4211.90.45149830.9540.1350.4711.08100
2.42-2.6611.70.29450070.970.0880.3081.044100
2.66-3.0412.50.20450460.9810.0590.2130.965100
3.04-3.8312.20.13450700.9930.0390.1390.736100
3.83-5011.80.09553410.9920.0290.10.90999.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.31 Å45.07 Å
Translation5.31 Å45.07 Å

-
Processing

Software
NameVersionClassification
HKL-3000data reduction
HKL-3000data scaling
PHASER2.6.0phasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JN6

6jn6


Resolution: 1.789→45.066 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2464 1999 4.71 %
Rwork0.2053 40399 -
obs0.2073 42398 85.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.89 Å2 / Biso mean: 29.3913 Å2 / Biso min: 7.27 Å2
Refinement stepCycle: final / Resolution: 1.789→45.066 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3456 0 43 250 3749
Biso mean--40.3 32.19 -
Num. residues----462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0193596
X-RAY DIFFRACTIONf_angle_d1.134897
X-RAY DIFFRACTIONf_chiral_restr0.062562
X-RAY DIFFRACTIONf_plane_restr0.008642
X-RAY DIFFRACTIONf_dihedral_angle_d13.0182078
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7893-1.83410.3066100.40581876
1.8341-1.88370.3883530.3506109733
1.8837-1.93910.33651160.2925233770
1.9391-2.00170.3051520.2678306792
2.0017-2.07320.27651610.2535323797
2.0732-2.15620.28641650.2434334199
2.1562-2.25440.29621630.23263309100
2.2544-2.37320.30091660.2223354100
2.3732-2.52190.25831670.21323365100
2.5219-2.71660.24521650.20673341100
2.7166-2.98990.25371670.20273378100
2.9899-3.42250.23351660.18713373100
3.4225-4.31140.19881720.16163453100
4.3114-45.0660.21161760.1838356099

+
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