[English] 日本語
Yorodumi
- PDB-6o5t: Crystal Structure of VIM-2 with Compound 16 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6o5t
TitleCrystal Structure of VIM-2 with Compound 16
ComponentsBeta-lactamase class B VIM-2
KeywordsHYDROLASE/INHIBITOR / Carbapenemase / Phosphonate / inhibitor / complex / 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 / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
ACETATE ION / Chem-L8J / Beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAkhtar, A. / Chen, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)Al103158 United States
CitationJournal: J.Med.Chem. / Year: 2019
Title: Heteroaryl Phosphonates as Noncovalent Inhibitors of Both Serine- and Metallocarbapenemases.
Authors: Pemberton, O.A. / Jaishankar, P. / Akhtar, A. / Adams, J.L. / Shaw, L.N. / Renslo, A.R. / Chen, Y.
History
DepositionMar 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)53,11719
Polymers51,3872
Non-polymers1,73017
Water3,459192
1
A: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5299
Polymers25,6931
Non-polymers8368
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)26,58810
Polymers25,6931
Non-polymers8959
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.389, 79.185, 67.501
Angle α, β, γ (deg.)90.000, 130.600, 90.000
Int Tables number5
Space group name H-MC121

-
Components

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


Mass: 25693.488 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, VIM-2, vim-2
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9K2N0
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: Zn
#3: Chemical ChemComp-L8J / [(5,7-dibromo-2-oxo-1,2-dihydroquinolin-4-yl)methyl]phosphonic acid


Mass: 396.957 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H8Br2NO4P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M Calcium Acetate, 20%(w/v) PEG-3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 23884 / % possible obs: 99.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.052 / Rrim(I) all: 0.101 / Χ2: 0.628 / Net I/σ(I): 5.2 / Num. measured all: 88997
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.143.10.32911120.840.2130.3940.43895
2.14-2.183.30.31611930.8660.2010.3750.4297.4
2.18-2.223.40.3111640.8910.1940.3660.42799.1
2.22-2.263.60.31111890.9110.1920.3670.41999.7
2.26-2.313.80.26712000.9270.1610.3120.41599.9
2.31-2.373.80.24111850.9390.1450.2820.44100
2.37-2.423.80.22411970.9510.1340.2620.451100
2.42-2.493.80.19812130.9540.1180.230.472100
2.49-2.563.80.1911680.9560.1130.2220.473100
2.56-2.653.80.16211930.9750.0960.1890.512100
2.65-2.743.80.14112100.9780.0840.1650.515100
2.74-2.853.80.12311920.9850.0730.1440.558100
2.85-2.983.80.1112040.9830.0660.1290.59100
2.98-3.143.80.09411910.990.0560.110.672100
3.14-3.333.80.07911940.9910.0470.0920.818100
3.33-3.593.80.06412250.9950.0380.0750.862100
3.59-3.953.80.05511840.9950.0330.0650.851100
3.95-4.523.80.0512050.9960.0290.0580.944100
4.52-5.73.80.04712220.9970.0280.0550.951100
5.7-503.80.04712430.9970.0280.0551.15499.9

-
Processing

Software
NameVersionClassification
PHENIX1.14_3228refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4bz3

4bz3


Resolution: 2.1→39.593 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 24.57
RfactorNum. reflection% reflection
Rfree0.236 2029 8.5 %
Rwork0.1789 --
obs0.1838 23880 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.91 Å2 / Biso mean: 28.9246 Å2 / Biso min: 9.65 Å2
Refinement stepCycle: final / Resolution: 2.1→39.593 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3506 0 85 192 3783
Biso mean--44.25 31.67 -
Num. residues----466
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0975-2.14990.27551350.19871442157793
2.1499-2.2080.30121410.20481524166598
2.208-2.2730.29931460.211315681714100
2.273-2.34640.26411450.198215491694100
2.3464-2.43020.24621460.196315771723100
2.4302-2.52750.27571410.194515581699100
2.5275-2.64250.27141510.195915651716100
2.6425-2.78180.27591420.196815701712100
2.7818-2.9560.2491500.186615901740100
2.956-3.18420.25131420.190215461688100
3.1842-3.50440.20371500.173115721722100
3.5044-4.01110.23871440.162715931737100
4.0111-5.05190.19231470.14415801727100
5.0519-39.59950.19721490.17516171766100

+
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