[English] 日本語
Yorodumi
- PDB-8pgt: Crystal structure of the metallo-beta-lactamase VIM1 with 3393 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8pgt
TitleCrystal structure of the metallo-beta-lactamase VIM1 with 3393
ComponentsBeta-lactamase VIM-1
KeywordsANTIMICROBIAL PROTEIN / Complex / metallo-beta-lactamase / inhibitor / zinc / indole carboxylate
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
: / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsCalvopina, K. / Brem, J. / Farley, A.J.M. / Allen, M.D. / Schofield, C.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust099141/Z/12/Z United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of the metallo-beta-lactamase VIM1 with 3393
Authors: Calvopina, K. / Brem, J. / Farley, A.J.M. / Allen, M.D. / Schofield, C.J.
History
DepositionJun 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-lactamase VIM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6194
Polymers28,0511
Non-polymers5673
Water5,963331
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-79 kcal/mol
Surface area9540 Å2
Unit cell
Length a, b, c (Å)39.490, 68.010, 40.300
Angle α, β, γ (deg.)90.000, 93.750, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein Beta-lactamase VIM-1 / Class B carbapenemase VIM-1 / Metallo-beta-lactamase / Metallo-beta-lactamase VIM-1 / Metallobeta- ...Class B carbapenemase VIM-1 / Metallo-beta-lactamase / Metallo-beta-lactamase VIM-1 / Metallobeta-lactamase / Subclass B1 metallo-beta-lactamase VIM-1 / VIM-1 / VIM-1 metallo-beta-lactamase / VIM-1 protein


Mass: 28051.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: blaVIM, blaVIM-1, CAZ10_38240, CAZ10_38245 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q9XAY4
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-YKZ / 7-[(1~{S})-1-[2-(aminomethyl)-6-oxidanylidene-5-oxa-7-azaspiro[3.4]octan-7-yl]ethyl]-3-(5-oxidanylpyridin-3-yl)-1~{H}-indole-2-carboxylic acid


Mass: 436.460 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H24N4O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 1.93 Å3/Da / Density % sol: 36.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 2.2M ammonium phosphate 0.1M TrisHCl, pH 8.5 / PH range: 8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97965 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97965 Å / Relative weight: 1
ReflectionResolution: 1.21→40.21 Å / Num. obs: 62965 / % possible obs: 97.4 % / Redundancy: 6.4 % / Biso Wilson estimate: 12.16 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.02 / Rrim(I) all: 0.051 / Net I/σ(I): 18.3
Reflection shellResolution: 1.21→1.24 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 3525 / CC1/2: 0.933 / Rpim(I) all: 0.144 / Rrim(I) all: 0.292 / % possible all: 74.7

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.21→40.21 Å / SU ML: 0.0763 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 11.7347
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1374 3132 4.98 %
Rwork0.1186 59799 -
obs0.1195 62931 97.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17 Å2
Refinement stepCycle: LAST / Resolution: 1.21→40.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1731 0 34 331 2096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01552071
X-RAY DIFFRACTIONf_angle_d1.44772872
X-RAY DIFFRACTIONf_chiral_restr0.1129316
X-RAY DIFFRACTIONf_plane_restr0.0173388
X-RAY DIFFRACTIONf_dihedral_angle_d14.9097328
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.21-1.230.1702970.12452004X-RAY DIFFRACTION71.66
1.23-1.250.12711220.12272218X-RAY DIFFRACTION81.05
1.25-1.270.16771500.11122503X-RAY DIFFRACTION90.15
1.27-1.290.16731150.10512750X-RAY DIFFRACTION98.42
1.29-1.320.14551350.09992831X-RAY DIFFRACTION99.97
1.32-1.350.12551530.0982746X-RAY DIFFRACTION100
1.35-1.370.12861590.0922775X-RAY DIFFRACTION100
1.37-1.410.12211340.08882814X-RAY DIFFRACTION100
1.41-1.440.12861540.08952770X-RAY DIFFRACTION99.97
1.44-1.480.14491670.08892765X-RAY DIFFRACTION99.97
1.48-1.520.11191680.08472759X-RAY DIFFRACTION100
1.52-1.570.11781310.0852833X-RAY DIFFRACTION99.97
1.57-1.630.12741620.08812735X-RAY DIFFRACTION100
1.63-1.70.12571350.09472802X-RAY DIFFRACTION99.97
1.7-1.770.12241300.09392815X-RAY DIFFRACTION99.97
1.77-1.870.12031350.10062807X-RAY DIFFRACTION100
1.87-1.980.11611260.10472819X-RAY DIFFRACTION99.86
1.98-2.140.131230.10732820X-RAY DIFFRACTION100
2.14-2.350.141510.11232800X-RAY DIFFRACTION99.93
2.35-2.690.1261740.12492776X-RAY DIFFRACTION100
2.69-3.390.15161710.13842794X-RAY DIFFRACTION100
3.39-40.210.15641400.15862863X-RAY DIFFRACTION99.64

+
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