[English] 日本語
Yorodumi
- PDB-6itx: Structure of the C-terminal head domain of the avian adenovirus E... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6itx
TitleStructure of the C-terminal head domain of the avian adenovirus EDSV fiber
ComponentsFiber proteinFibrous protein
KeywordsCELL ADHESION / avian adenovirus / fiber protein
Function / homology
Function and homology information


adhesion receptor-mediated virion attachment to host cell / viral capsid / cell adhesion / symbiont entry into host cell / host cell nucleus
Similarity search - Function
Fiber protein 1, C-terminal domain / Fiber protein 1, C-terminal / Fiber protein, C-terminal domain superfamily / C-terminal head domain of the fowl adenovirus type 1 long fibre / Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein / Attachment protein shaft domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
GLUTAMINE / Fiber protein / Fiber protein
Similarity search - Component
Biological speciesDuck adenovirus 1
MethodX-RAY DIFFRACTION / Resolution: 2.75 Å
AuthorsWei, Q. / Song, Y.
Funding support China, 1items
OrganizationGrant numberCountry
China
CitationJournal: Int.J.Biol.Macromol. / Year: 2019
Title: Unravelling the receptor binding property of egg drop syndrome virus (EDSV) from the crystal structure of EDSV fiber head.
Authors: Song, Y. / Wei, Q. / Liu, Y. / Feng, H. / Chen, Y. / Wang, Y. / Bai, Y. / Xing, G. / Deng, R. / Zhang, G.
History
DepositionNov 26, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2019Provider: 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: Fiber protein
B: Fiber protein
D: Fiber protein
C: Fiber protein
E: Fiber protein
F: Fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,81716
Polymers192,6066
Non-polymers1,21110
Water4,594255
1
A: Fiber protein
B: Fiber protein
C: Fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7877
Polymers96,3033
Non-polymers4844
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-69 kcal/mol
Surface area24750 Å2
MethodPISA
2
D: Fiber protein
E: Fiber protein
F: Fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,0299
Polymers96,3033
Non-polymers7276
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7090 Å2
ΔGint-94 kcal/mol
Surface area25450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.515, 63.236, 165.806
Angle α, β, γ (deg.)90.000, 93.540, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Fiber protein / Fibrous protein / EDSV fiber


Mass: 32100.943 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Duck adenovirus 1 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: S4TZM6, UniProt: O11424*PLUS
#2: Chemical
ChemComp-GLN / GLUTAMINE / Glutamine


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C5H10N2O3
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.86 Å3/Da / Density % sol: 56.92 %
Crystal growTemperature: 293.15 K / Method: evaporation / Details: 0.2M Potassium sulfate, 15% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 285 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: May 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.75→30 Å / Num. obs: 57643 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 46.9 Å2 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.051 / Rrim(I) all: 0.131 / Χ2: 0.99 / Net I/σ(I): 5.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.75-2.85.70.47328300.8990.2150.5210.96399.6
2.8-2.855.90.41428240.9310.1840.4540.97599.4
2.85-2.96.40.39928800.9440.1690.4340.99699.6
2.9-2.966.70.37428260.9560.1560.4060.95599.6

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
AMoREphasing
RefinementResolution: 2.75→29.882 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.28
RfactorNum. reflection% reflection
Rfree0.2316 2902 5.08 %
Rwork0.1922 --
obs0.1943 57130 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 122.8 Å2 / Biso mean: 46.6149 Å2 / Biso min: 13.64 Å2
Refinement stepCycle: final / Resolution: 2.75→29.882 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9920 0 70 255 10245
Biso mean--64.16 41.91 -
Num. residues----1313
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810272
X-RAY DIFFRACTIONf_angle_d1.00314086
X-RAY DIFFRACTIONf_chiral_restr0.0551599
X-RAY DIFFRACTIONf_plane_restr0.0071816
X-RAY DIFFRACTIONf_dihedral_angle_d13.4085866
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7377-2.78250.34121010.23362015211678
2.7825-2.83050.29281340.2242419255394
2.8305-2.88190.28721230.21962557268097
2.8819-2.93730.31211270.22782610273799
2.9373-2.99720.29751450.23482585273099
2.9972-3.06230.26021550.224725542709100
3.0623-3.13340.27161500.211726182768100
3.1334-3.21170.24161500.197225642714100
3.2117-3.29850.23181370.196626492786100
3.2985-3.39540.25711170.197325922709100
3.3954-3.50480.25721330.18842635276899
3.5048-3.62990.23491390.19092570270999
3.6299-3.77490.21551310.182126402771100
3.7749-3.94640.22571580.177726442802100
3.9464-4.15390.21440.169825802724100
4.1539-4.41340.15271380.156926372775100
4.4134-4.75290.20821330.158626382771100
4.7529-5.22890.1871600.161326252785100
5.2289-5.98030.23291490.186626492798100
5.9803-7.51470.26481290.209326912820100
7.5147-29.8840.24151490.231727562905100

+
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