[English] 日本語
Yorodumi
- PDB-2j2j: Canine adenovirus fibre head at 1.5 A resolution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2j2j
TitleCanine adenovirus fibre head at 1.5 A resolution
ComponentsFIBER PROTEIN
KeywordsVIRAL PROTEIN / FIBER PROTEIN / CANINE ADENOVIRUS / AD / CAR / KNOB / HEAD / FIBER FIBRE / ADENOVIRUS / COXSACKIEVIRUS / ADENOVIRUS RECEPTOR
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
Adenovirus pIV-related, attachment domain / Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein, knob / Adenoviral fibre protein (knob domain) / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein / Attachment protein shaft domain superfamily / Adenovirus pIV-like, attachment domain / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesCANINE ADENOVIRUS 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSeiradake, E. / Lortat-Jacob, H. / Billet, O. / Kremer, E.J. / Cusack, S.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structural and Mutational Analysis of Human Ad37 and Canine Adenovirus 2 Fiber Heads in Complex with the D1 Domain of Coxsackie and Adenovirus Receptor.
Authors: Seiradake, E. / Lortat-Jacob, H. / Billet, O. / Kremer, E.J. / Cusack, S.
History
DepositionAug 16, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FIBER PROTEIN
B: FIBER PROTEIN
C: FIBER PROTEIN
D: FIBER PROTEIN
E: FIBER PROTEIN
F: FIBER PROTEIN


Theoretical massNumber of molelcules
Total (without water)130,1136
Polymers130,1136
Non-polymers00
Water27,7251539
1
A: FIBER PROTEIN
B: FIBER PROTEIN
D: FIBER PROTEIN


Theoretical massNumber of molelcules
Total (without water)65,0573
Polymers65,0573
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: FIBER PROTEIN
E: FIBER PROTEIN
F: FIBER PROTEIN


Theoretical massNumber of molelcules
Total (without water)65,0573
Polymers65,0573
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)55.834, 88.547, 106.913
Angle α, β, γ (deg.)90.00, 96.40, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.50834, -0.72708, -0.46146), (0.18875, -0.42876, 0.88348), (-0.84022, -0.53621, -0.08071)19.06372, 18.89393, 21.68553
2given(0.97429, 0.00013, 0.22528), (0.00047, -1, -0.00149), (0.22528, 0.00155, -0.97429)-6.14509, 0.13482, 52.97097
3given(0.50776, 0.19911, -0.83817), (-0.72609, -0.4247, -0.54075), (-0.46365, 0.88317, -0.07107)4.8635, 33.52853, -6.21569
4given(0.30452, -0.82985, -0.46756), (-0.18985, 0.42814, -0.88354), (0.93339, 0.35782, -0.02717)17.32383, -18.75992, 36.22797
5given(0.39169, 0.39091, -0.83293), (0.72678, 0.4237, 0.54062), (0.56424, -0.81711, -0.11815)-2.69801, -33.3956, 60.24168

-
Components

#1: Protein
FIBER PROTEIN / PIV / CANINE ADENOVIRUS 2 FIBRE HEAD


Mass: 21685.541 Da / Num. of mol.: 6 / Fragment: FIBRE HEAD DOMAIN, RESIDUES 358-542
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CANINE ADENOVIRUS 2 / Plasmid: PQE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 / References: UniProt: Q65914
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1539 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCONTAINS ONLY FIBRE HEAD DOMAIN, AND N-TERMINAL 6XHIS TAG

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44 %
Crystal growDetails: 0.15 M KBR, 30% PEG MONOMETHYL-ETHER 2000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.5→28.4 Å / Num. obs: 156532 / % possible obs: 95.1 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 8.1 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.3
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 7.8 / % possible all: 89.4

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QHV

1qhv


Resolution: 1.5→106 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.918 / SU B: 2.675 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.206 3156 2 %RANDOM
Rwork0.165 ---
obs0.165 153376 94.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 6.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å20.04 Å2
2--0.11 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.5→106 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8436 0 0 1539 9975
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0228685
X-RAY DIFFRACTIONr_bond_other_d0.0010.025817
X-RAY DIFFRACTIONr_angle_refined_deg1.4231.94611861
X-RAY DIFFRACTIONr_angle_other_deg0.902314186
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.02151100
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.71923.684361
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.034151362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.8271554
X-RAY DIFFRACTIONr_chiral_restr0.0870.21355
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029695
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021795
X-RAY DIFFRACTIONr_nbd_refined0.2190.21589
X-RAY DIFFRACTIONr_nbd_other0.2040.26352
X-RAY DIFFRACTIONr_nbtor_refined0.1740.24440
X-RAY DIFFRACTIONr_nbtor_other0.0830.24602
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.21096
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3180.2109
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.291
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2831.57018
X-RAY DIFFRACTIONr_mcbond_other0.3961.52209
X-RAY DIFFRACTIONr_mcangle_it1.53828932
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.31533804
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1224.52922
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.207 235 -
Rwork0.145 10568 -
obs--88.92 %

+
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