[English] 日本語
Yorodumi
- PDB-5x5v: Crystal structure of pseudorabies virus glycoprotein D -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5x5v
TitleCrystal structure of pseudorabies virus glycoprotein D
ComponentsGD
KeywordsVIRAL PROTEIN / herpes simplex virus / pseudorabies virus / glycoprotein D
Function / homologyHerpesvirus glycoprotein D/GG/GX domain / Herpesvirus glycoprotein D/GG/GX domain / Immunoglobulin-like domain superfamily / membrane / GD
Function and homology information
Biological speciesSuid herpesvirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLi, A. / Lu, G. / Qi, J. / Wu, L. / Tian, K. / Luo, T. / Shi, Y. / Yan, J. / Gao, G.F.
CitationJournal: To Be Published
Title: Crystal structure of pseudorabies virus glycoprotein D
Authors: Li, A. / Lu, G. / Qi, J. / Wu, L. / Tian, K. / Luo, T. / Shi, Y. / Yan, J. / Gao, G.F.
History
DepositionFeb 17, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GD


Theoretical massNumber of molelcules
Total (without water)44,5851
Polymers44,5851
Non-polymers00
Water6,017334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12610 Å2
2
A: GD

A: GD


Theoretical massNumber of molelcules
Total (without water)89,1702
Polymers89,1702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_658-x+1,y,-z+31
Buried area2450 Å2
ΔGint-13 kcal/mol
Surface area22770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.398, 60.975, 60.681
Angle α, β, γ (deg.)90.00, 111.22, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-519-

HOH

21A-711-

HOH

-
Components

#1: Protein GD / glycoprotein D


Mass: 44584.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Suid herpesvirus 1 / Strain: Becker / Gene: US6 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: G3G933
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 1.54 Å3/Da / Density % sol: 19.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M ammonium acetate 0.1 M bis-tris pH 5.5 17 % PEG 10,000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 42212 / % possible obs: 97.6 % / Redundancy: 6.1 % / Net I/σ(I): 25.5
Reflection shellResolution: 1.5→1.55 Å / CC1/2: 0.966 / Rpim(I) all: 0.129

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C36

2c36


Resolution: 1.5→23.531 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.46
RfactorNum. reflection% reflection
Rfree0.1923 2130 5.05 %
Rwork0.1691 --
obs0.1703 42206 97.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→23.531 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1925 0 0 334 2259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062006
X-RAY DIFFRACTIONf_angle_d1.092743
X-RAY DIFFRACTIONf_dihedral_angle_d12.406738
X-RAY DIFFRACTIONf_chiral_restr0.042281
X-RAY DIFFRACTIONf_plane_restr0.006362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.53490.23261270.19592635X-RAY DIFFRACTION96
1.5349-1.57330.18631030.17912669X-RAY DIFFRACTION97
1.5733-1.61580.19281320.182697X-RAY DIFFRACTION97
1.6158-1.66330.19021490.17052620X-RAY DIFFRACTION97
1.6633-1.7170.20471310.16922676X-RAY DIFFRACTION97
1.717-1.77830.19561450.16812655X-RAY DIFFRACTION98
1.7783-1.84950.18521370.17372712X-RAY DIFFRACTION98
1.8495-1.93370.2151410.17432654X-RAY DIFFRACTION98
1.9337-2.03550.2421530.16662675X-RAY DIFFRACTION98
2.0355-2.1630.17831530.16152704X-RAY DIFFRACTION99
2.163-2.32990.18231510.17122702X-RAY DIFFRACTION99
2.3299-2.56410.20271560.16862709X-RAY DIFFRACTION99
2.5641-2.93450.21691690.17862711X-RAY DIFFRACTION99
2.9345-3.69490.17461370.16362740X-RAY DIFFRACTION99
3.6949-23.53360.17531460.16472517X-RAY DIFFRACTION90
Refinement TLS params.Method: refined / Origin x: -4.1506 Å / Origin y: -67.6526 Å / Origin z: 71.3213 Å
111213212223313233
T0.1185 Å20.0096 Å2-0.0031 Å2-0.0981 Å2-0.0083 Å2--0.1104 Å2
L1.144 °2-0.0101 °20.1049 °2-0.5552 °2-0.0955 °2--0.8134 °2
S0.0476 Å °0.1345 Å °0.0031 Å °-0.0318 Å °-0.0532 Å °0.0552 Å °0.012 Å °-0.0111 Å °0.0008 Å °
Refinement TLS groupSelection details: all

+
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