[English] 日本語
Yorodumi
- PDB-7chu: Geobacillus virus E2 - ORF18 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7chu
TitleGeobacillus virus E2 - ORF18
ComponentsPutative pectin lyase
KeywordsCELL INVASION / Tailspike protein / Thermophilic bacteriophage
Function / homologyPectate lyase superfamily protein / Pectate lyase superfamily protein / Pectin lyase fold / Pectin lyase fold/virulence factor / lyase activity / Putative pectin lyase
Function and homology information
Biological speciesGeobacillus virus E2
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.008 Å
AuthorsGong, Y.
CitationJournal: Int.J.Biol.Macromol. / Year: 2020
Title: Structural and functional characterization of the deep-sea thermophilic bacteriophage GVE2 tailspike protein.
Authors: Zhang, L. / Yan, Y. / Gan, Q. / She, Z. / Zhu, K. / Wang, J. / Gao, Z. / Dong, Y. / Gong, Y.
History
DepositionJul 6, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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
A: Putative pectin lyase
B: Putative pectin lyase
C: Putative pectin lyase


Theoretical massNumber of molelcules
Total (without water)170,0883
Polymers170,0883
Non-polymers00
Water23,8881326
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24000 Å2
ΔGint-161 kcal/mol
Surface area47460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.842, 150.808, 84.707
Angle α, β, γ (deg.)90.000, 95.140, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Putative pectin lyase /


Mass: 56695.992 Da / Num. of mol.: 3 / Fragment: tail spike protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus virus E2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A6M964
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1326 / 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: 2.39 Å3/Da / Density % sol: 48.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M HEPES, 0.2M sodium chloride, pH 7.5, 25% (w/v) polyethylene glycol 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→36.7 Å / Num. obs: 101736 / % possible obs: 95.8 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 16.9
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.54 / Num. unique obs: 2846

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.008→36.698 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 20.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1958 5077 4.99 %
Rwork0.158 96659 -
obs0.1598 101736 95.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.53 Å2 / Biso mean: 23.2745 Å2 / Biso min: 5.63 Å2
Refinement stepCycle: final / Resolution: 2.008→36.698 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11910 0 0 1326 13236
Biso mean---31.03 -
Num. residues----1551
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.008-2.03060.2241410.1716278683
2.0306-2.05450.23211620.1676331799
2.0545-2.07950.19931860.1702329099
2.0795-2.10580.22221820.1676329598
2.1058-2.13350.20741720.1625328598
2.1335-2.16280.2241620.1551333399
2.1628-2.19360.21961730.1645329198
2.1936-2.22640.27921450.1936320496
2.2264-2.26120.40161040.3154201460
2.2612-2.29820.24121840.1872308192
2.2982-2.33790.21191720.1544330999
2.3379-2.38040.19341790.1508326298
2.3804-2.42610.18711610.15328598
2.4261-2.47570.22781480.1536335099
2.4757-2.52950.21681820.1593330699
2.5295-2.58830.24161900.1602325798
2.5883-2.6530.20361700.1627332898
2.653-2.72470.23182060.1602322498
2.7247-2.80490.19481760.1642329598
2.8049-2.89540.20341940.1631333698
2.8954-2.99880.18681740.1567330299
2.9988-3.11880.18691660.1624332699
3.1188-3.26070.20951780.1643335499
3.2607-3.43250.17971750.1543330999
3.4325-3.64730.16621620.1433328297
3.6473-3.92860.17861440.1544282384
3.9286-4.32340.13811670.1196323696
4.3234-4.94780.1331690.1153396100
4.9478-6.22870.17591730.15823365100
6.2287-36.6980.18151800.173341899

+
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