[English] 日本語
Yorodumi
- PDB-6n7o: Crystal structure of GIL01 gp7 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6n7o
TitleCrystal structure of GIL01 gp7
ComponentsGIL01 gp7
KeywordsVIRAL PROTEIN
Function / homologyIODIDE ION / Gene regulator
Function and homology information
Biological speciesBacillus phage pGIL01 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsCaveney, N.A. / Strynadka, N.C.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Structure / Year: 2019
Title: Structural Insights into Bacteriophage GIL01 gp7 Inhibition of Host LexA Repressor.
Authors: Caveney, N.A. / Pavlin, A. / Caballero, G. / Bahun, M. / Hodnik, V. / de Castro, L. / Fornelos, N. / Butala, M. / Strynadka, N.C.J.
History
DepositionNov 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: GIL01 gp7
A: GIL01 gp7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5315
Polymers12,1502
Non-polymers3813
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-17 kcal/mol
Surface area5180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.690, 44.700, 46.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein GIL01 gp7


Mass: 6074.929 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage pGIL01 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7WSG2
#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 1.69 Å3/Da / Density % sol: 27.2 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M sodium iodide, 0.1 M Bis Tris propane, pH 8.5, 20% (w/v) PEG 3.35k

-
Data collection

DiffractionMean temperature: 85 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.9801 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.47→32.158 Å / Num. obs: 9511 / % possible obs: 99.1 % / Redundancy: 7.497 % / Biso Wilson estimate: 21.25 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.221 / Rrim(I) all: 0.237 / Χ2: 0.97 / Net I/σ(I): 7.24 / Num. measured all: 108259
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.47-1.515.6134.1450.449560.1544.5891.4
1.51-1.556.7573.1070.6810033.37196.5
1.55-1.598.0052.9350.819980.223.137100
1.59-1.648.1212.3131.139870.2912.47100
1.64-1.78.0631.9141.419410.5152.045100
1.7-1.768.041.7391.749090.5391.859100
1.76-1.827.9441.3372.488770.7631.43100
1.82-1.97.9011.0333.728720.8781.105100
1.9-1.987.9060.7925.28080.9050.847100
1.98-2.087.8570.6347.147950.9260.679100
2.08-2.197.7660.4439.487450.9490.475100
2.19-2.327.5480.32811.767250.9730.352100
2.32-2.487.5510.27912.896720.9820.3100
2.48-2.687.4920.2115.016220.9810.22699.8
2.68-2.947.3580.16216.245830.9890.174100
2.94-3.297.2430.12318.165390.9910.133100
3.29-3.86.8820.08421.074760.9950.09199.8
3.8-4.656.8180.0822.474070.9930.08699.8
4.65-6.576.9350.07921.393250.9920.08599.4
6.57-32.1586.1750.06721.642000.9970.073100

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→32.158 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.86
RfactorNum. reflection% reflection
Rfree0.2297 476 5.01 %
Rwork0.1933 --
obs0.1951 9508 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 80.41 Å2 / Biso mean: 27.3025 Å2 / Biso min: 13.47 Å2
Refinement stepCycle: final / Resolution: 1.7→32.158 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms605 0 3 71 679
Biso mean--31.5 36.83 -
Num. residues----75
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006667
X-RAY DIFFRACTIONf_angle_d0.678901
X-RAY DIFFRACTIONf_chiral_restr0.039106
X-RAY DIFFRACTIONf_plane_restr0.003113
X-RAY DIFFRACTIONf_dihedral_angle_d18.177277
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7-1.9460.30821550.269129493104
1.946-2.45160.231570.204629813138
2.4516-32.16420.21051640.172731023266

+
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