[English] 日本語
Yorodumi
- PDB-1ocy: Structure of the receptor-binding domain of the bacteriophage T4 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ocy
TitleStructure of the receptor-binding domain of the bacteriophage T4 short tail fibre
ComponentsBACTERIOPHAGE T4 SHORT TAIL FIBRE
KeywordsSTRUCTURAL PROTEIN / FIBROUS PROTEIN / LIPO-POLYSACCHARIDE BINDING / BACTERIOPHAGE STRUCTURAL PROTEIN / BASEPLATE PROTEIN / GENE PRODUCT 12
Function / homology
Function and homology information


virus tail, baseplate / virus tail, fiber / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / metal ion binding
Similarity search - Function
receptor-binding domain of the bacteriophage t4 short tail fibre, domain 2 / receptor-binding domain of the bacteriophage t4 short tail fibre, domain 2 / heat- and protease-stable fragment of the bacteriophage t4 short fibre, domain 3 / Phage tail collar domain / Bacteriophage T4, Gp12 / Short tail fibre protein, C-terminal / Short tail fibre protein, C-terminal superfamily / Phage short tail fibre protein gp12, middle domain / Short tail fibre protein receptor-binding domain / Phage tail collar domain ...receptor-binding domain of the bacteriophage t4 short tail fibre, domain 2 / receptor-binding domain of the bacteriophage t4 short tail fibre, domain 2 / heat- and protease-stable fragment of the bacteriophage t4 short fibre, domain 3 / Phage tail collar domain / Bacteriophage T4, Gp12 / Short tail fibre protein, C-terminal / Short tail fibre protein, C-terminal superfamily / Phage short tail fibre protein gp12, middle domain / Short tail fibre protein receptor-binding domain / Phage tail collar domain / Phage tail collar domain superfamily / Phage Tail Collar Domain / Few Secondary Structures / Irregular / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Short tail fiber protein gp12 / Gp12
Similarity search - Component
Biological speciesBACTERIOPHAGE T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.5 Å
AuthorsThomassen, E. / Gielen, G. / Schuetz, M. / Miller, S. / van Raaij, M.J.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: The Structure of the Receptor-Binding Domain of the Bacteriophage T4 Short Tail Fibre Reveals a Knitted Trimeric Metal-Binding Fold
Authors: Thomassen, E. / Gielen, G. / Schuetz, M. / Schoehn, G. / Abrahams, J.P. / Miller, S. / van Raaij, M.J.
#1: Journal: J.Mol.Biol. / Year: 2001
Title: Crystal Structure of a Heat- and Protease-Stable Part of the Bacteriophage T4 Short Tail Fibre
Authors: van Raaij, M.J. / Schoehn, G. / Burda, M.R. / Miller, S.
#2: Journal: Biol.Chem. / Year: 2001
Title: Identification and Crystallisation of a Heat- and Protease-Stable Fragment of the Bacteriophage T4 Short Tail Fibre
Authors: van Raaij, M.J. / Schoehn, G. / Jaquinod, M. / Ashman, K. / Burda, M.R. / Miller, S.
#3: Journal: Biol.Chem. / Year: 2000
Title: Stability of Bacteriophage T4 Short Tail Fiber
Authors: Burda, M.R. / Hindennach, I. / Miller, S.
#4: Journal: Eur.J.Biochem. / Year: 1999
Title: Folding of Coliphage T4 Short Tail Fiber in Vitro. Analysing the Role of a Bacteriophage-Encoded Chaperone
Authors: Burda, M.R. / Miller, S.
History
DepositionFeb 11, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2018Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.page_last / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BACTERIOPHAGE T4 SHORT TAIL FIBRE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2955
Polymers21,8451
Non-polymers4504
Water9,296516
1
A: BACTERIOPHAGE T4 SHORT TAIL FIBRE
hetero molecules

A: BACTERIOPHAGE T4 SHORT TAIL FIBRE
hetero molecules

A: BACTERIOPHAGE T4 SHORT TAIL FIBRE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,88415
Polymers65,5353
Non-polymers1,34912
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)50.782, 50.782, 435.647
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-1530-

SO4

21A-1531-

ZN

31A-2264-

HOH

41A-2354-

HOH

51A-2355-

HOH

61A-2447-

HOH

71A-2452-

HOH

81A-2515-

HOH

-
Components

#1: Protein BACTERIOPHAGE T4 SHORT TAIL FIBRE


Mass: 21845.139 Da / Num. of mol.: 1 / Fragment: RECEPTOR-BINDING DOMAIN, RESIDUES 330-527
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTERIOPHAGE T4 (virus) / Strain: D
Description: VARIANT AS PRESENT IN LABORATORY OF S. MILLER. CO-EXPRESSION WITH GP57 CHAPERONE
Plasmid: PET21+ / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 / Variant (production host): DE3 / References: UniProt: Q38160, UniProt: P10930*PLUS
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 516 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsT4D STRAIN VARIANT, SEQUENCE ANALYSIS OF EXPRESSION PLASMID PERFORMED IN THE LABORATORY OF S. MILLER

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 64 %
Crystal growpH: 5.6
Details: 15-25 % (V/V),2-METHYLPROPANE-2-OL (TERTIARY BUTANOL), 100 MM SODIUM CITRATE PH 5.6, 10% (V/V) GLYCEROL,10 MM HEPES, 150 MM SODIUM CHLORIDE
Crystal grow
*PLUS
pH: 5.6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110-20 mg/mlprotein1drop
215-35 %(v/v)tertiary butanol1reservoir
3100 mMsodium citrate1reservoirpH5.6
40-10 %(v/v)glycerol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9464
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 13, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9464 Å / Relative weight: 1
ReflectionResolution: 1.5→15 Å / Num. obs: 96264 / % possible obs: 89.8 % / Redundancy: 6.56 % / Biso Wilson estimate: 14.103 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 4.122
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 3.13 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.37 / % possible all: 53.3
Reflection
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 15 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.106
Reflection shell
*PLUS
% possible obs: 53.3 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.284

-
Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
SOLVE/RESOLVEphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.5→15 Å / SU B: 0.5303 / SU ML: 0.0194 / Cross valid method: THROUGHOUT / ESU R: 0.0375 / ESU R Free: 0.0354
Details: RESIDUES 85-329 COULD NOT BE MODELLED DUE TO DISORDER
RfactorNum. reflection% reflectionSelection details
Rfree0.1516 1922 2.066 %RANDOM
Rwork0.1434 ---
obs-94341 89.7582 %-
Displacement parametersBiso mean: 23.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20.18 Å20 Å2
2--0.36 Å20 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1537 0 24 516 2077
Refinement
*PLUS
Lowest resolution: 15 Å / Rfactor Rfree: 0.152 / Rfactor Rwork: 0.143
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.018
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.6
LS refinement shell
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 1.58 Å / Rfactor Rfree: 0.22 / Num. reflection Rfree: 116 / Rfactor Rwork: 0.2 / Num. reflection obs: 6339

+
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