[English] 日本語
Yorodumi
- PDB-1qex: BACTERIOPHAGE T4 GENE PRODUCT 9 (GP9), THE TRIGGER OF TAIL CONTRA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qex
TitleBACTERIOPHAGE T4 GENE PRODUCT 9 (GP9), THE TRIGGER OF TAIL CONTRACTION AND THE LONG TAIL FIBERS CONNECTOR
ComponentsPROTEIN (BACTERIOPHAGE T4 GENE PRODUCT 9 (GP9))
KeywordsVIRAL PROTEIN / BACTERIOPHAGE T4 / BASEPLATE / GENE PRODUCT 9 / OLIGOMERIZATION
Function / homology
Function and homology information


virus tail, baseplate / viral tail assembly / viral release from host cell
Similarity search - Function
Bacteriophage t4 gene product 9 (gp9) / gp9 / 4-oxalocrotonate tautomerase-like / Baseplate structural protein Gp9 C-terminal domain superfamily / Baseplate structural protein Gp9/Gp10 / Baseplate structural protein Gp9/Gp10 middle domain superfamily / Gp9-like superfamily / : / Bacteriophage T4 gp9/10-like protein, N-terminal / Bacteriophage T4 gp9/10-like protein, C-terminal ...Bacteriophage t4 gene product 9 (gp9) / gp9 / 4-oxalocrotonate tautomerase-like / Baseplate structural protein Gp9 C-terminal domain superfamily / Baseplate structural protein Gp9/Gp10 / Baseplate structural protein Gp9/Gp10 middle domain superfamily / Gp9-like superfamily / : / Bacteriophage T4 gp9/10-like protein, N-terminal / Bacteriophage T4 gp9/10-like protein, C-terminal / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Jelly Rolls / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Baseplate protein gp9
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 2.3 Å
AuthorsKostyuchenko, V.A. / Navruzbekov, G.A. / Kurochkina, L.P. / Strelkov, S.V. / Mesyanzhinov, V.V. / Rossmann, M.G.
Citation
Journal: Structure Fold.Des. / Year: 1999
Title: The structure of bacteriophage T4 gene product 9: the trigger for tail contraction.
Authors: Kostyuchenko, V.A. / Navruzbekov, G.A. / Kurochkina, L.P. / Strelkov, S.V. / Mesyanzhinov, V.V. / Rossmann, M.G.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization and preliminary crystallographic characterization of bacteriophage T4 baseplate protein encoded by gene 9.
Authors: Strelkov, S.V. / Zurabishvili, T.G. / Nepluev, I.V. / Efimov, V.P. / Isupov, M.N. / Harutyunyan, E.H. / Mesyanzhinov, V.V.
History
DepositionMar 30, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Oct 5, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Nov 20, 2019Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (BACTERIOPHAGE T4 GENE PRODUCT 9 (GP9))
B: PROTEIN (BACTERIOPHAGE T4 GENE PRODUCT 9 (GP9))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5264
Polymers62,0492
Non-polymers4772
Water5,260292
1
A: PROTEIN (BACTERIOPHAGE T4 GENE PRODUCT 9 (GP9))
B: PROTEIN (BACTERIOPHAGE T4 GENE PRODUCT 9 (GP9))
hetero molecules

A: PROTEIN (BACTERIOPHAGE T4 GENE PRODUCT 9 (GP9))
B: PROTEIN (BACTERIOPHAGE T4 GENE PRODUCT 9 (GP9))
hetero molecules

A: PROTEIN (BACTERIOPHAGE T4 GENE PRODUCT 9 (GP9))
B: PROTEIN (BACTERIOPHAGE T4 GENE PRODUCT 9 (GP9))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,57812
Polymers186,1486
Non-polymers1,4306
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area44770 Å2
ΔGint-239 kcal/mol
Surface area65280 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)94.330, 94.330, 440.940
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.49937, 0.86639, 0.00032), (0.86639, 0.49937, -0.00029), (-0.00041, 0.00013, -1)
Vector: 0.02251, -0.00543, 195.82069)

-
Components

#1: Protein PROTEIN (BACTERIOPHAGE T4 GENE PRODUCT 9 (GP9))


Mass: 31024.725 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: 9 / Plasmid: PET-23D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P10927
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 3.1 Å3/Da / Density % sol: 60 %
Crystal growpH: 7.5 / Details: 28% PEG-400 0.2M CACL2 HEPES-NA BUFFER, PH 7.5
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
228 %(v/v)PEG4001reservoir
30.2 M1reservoirCaCl2
40.1 Msodium HEPES1reservoir

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 1, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 33400 / % possible obs: 97.5 % / Observed criterion σ(I): -2 / Redundancy: 5.8 % / Biso Wilson estimate: 31.7 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 15
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 5 / % possible all: 96.3
Reflection shell
*PLUS
% possible obs: 96.3 %

-
Processing

Software
NameVersionClassification
CCP4model building
CNS0.5refinement
DENZOdata reduction
SnBphasing
CCP4phasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.3→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high rms absF: 5466890.49 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 2
Details: DISORDERED REGIONS WERE MODELLED STEREOCHEMICALLY AND MARKED BY HIGH B-FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1637 4.9 %RANDOM
Rwork0.239 ---
obs-33400 97.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.78 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 34.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.86 Å22.29 Å20 Å2
2--2.86 Å20 Å2
3----5.72 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.32 Å
Luzzati d res low-20 Å
Luzzati sigma a0.25 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4350 0 30 292 4672
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it2.222
X-RAY DIFFRACTIONc_scbond_it1.672
X-RAY DIFFRACTIONc_scangle_it2.432.5
LS refinement shellResolution: 2.3→2.4 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.304 223 5.5 %
Rwork0.28 3853 -
obs--96.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3HEPES.PARAMHEPES.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 4.9 % / Rfactor obs: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 34.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.86
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Highest resolution: 2.3 Å / Rfactor Rfree: 0.304 / % reflection Rfree: 5.5 % / Rfactor Rwork: 0.28

+
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