[English] 日本語
Yorodumi
- PDB-4uxf: Crystal structure of the carboxy-terminal region of the bacteriop... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4uxf
TitleCrystal structure of the carboxy-terminal region of the bacteriophage T4 proximal long tail fibre protein gp34, P21 native crystal
ComponentsLARGE TAIL FIBER PROTEIN P34
KeywordsVIRAL PROTEIN / CAUDOVIRALES / MYOVIRIDAE / TRIPLE BETA-HELIX
Function / homology: / Long-tail fiber proximal subunit, C-terminal, second / : / Long-tail fiber proximal subunit, C-terminal, trimerization domain / virus tail, fiber / Long-tail fiber proximal subunit
Function and homology information
Biological speciesENTEROBACTERIA PHAGE T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2 Å
AuthorsGranell, M. / Alvira, S. / Garcia-Doval, C. / Singh, A.K. / van Raaij, M.J.
Citation
Journal: Viruses / Year: 2017
Title: Crystal Structure of the Carboxy-Terminal Region of the Bacteriophage T4 Proximal Long Tail Fiber Protein Gp34.
Authors: Granell, M. / Namura, M. / Alvira, S. / Kanamaru, S. / van Raaij, M.J.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Crystallization of the Carboxy-Terminal Region of the Bacteriophage T4 Proximal Long Tail Fibre Protein Gp34.
Authors: Granell, M. / Namura, M. / Alvira, S. / Garcia-Doval, C. / Singh, A.K. / Gutsche, I. / Van Raaij, M.J. / Kanamaru, S.
History
DepositionAug 22, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Data collection
Revision 1.2Jul 12, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Aug 2, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.page_first ..._citation.journal_id_ISSN / _citation.page_first / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_database_status / struct_sheet / struct_site
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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: LARGE TAIL FIBER PROTEIN P34
B: LARGE TAIL FIBER PROTEIN P34
C: LARGE TAIL FIBER PROTEIN P34
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,32510
Polymers133,6803
Non-polymers6457
Water29,9771664
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area53250 Å2
ΔGint-275.9 kcal/mol
Surface area42680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.970, 76.050, 116.830
Angle α, β, γ (deg.)90.00, 99.12, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein LARGE TAIL FIBER PROTEIN P34 / PROXIMAL LONG TAIL FIBRE PROTEIN GP34 / PROTEIN GP34


Mass: 44559.973 Da / Num. of mol.: 3 / Fragment: CARBOXY-TERMINAL REGION, RESIDUES 894-1289
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTEROBACTERIA PHAGE T4 (virus)
Description: GERMAN COLLECTION OF MICROORGANISMS (DSMZ), DSM 4505
Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): PLYS / References: UniProt: P18771
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1664 / 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 %
Description: AN INTERMEDIATE MODEL OF RELATED PDB ENTRY 4UXE WAS USED AND REFINED AGAINST THE NATIVE DATA AFTER CHANGING SEMETS TO METS.
Crystal growpH: 8.5
Details: 10-16% (W/V) PEG 6000, 12-22% (V/V) GLYCEROL, 0.1 M TRIS-HCL PH 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 10, 2012 / Details: VERTICALLY BENDED MULTILAYER MIRRORS
RadiationMonochromator: DIAMOND (001) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 108802 / % possible obs: 99.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.1
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.3 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2→115.41 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.349 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.18676 2209 2 %THIN SHELLS
Rwork0.14647 ---
obs0.14732 106463 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.851 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å20 Å21.94 Å2
2--0 Å20 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 2→115.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9101 0 42 1664 10807
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.029404
X-RAY DIFFRACTIONr_bond_other_d0.0020.028690
X-RAY DIFFRACTIONr_angle_refined_deg1.5341.93212786
X-RAY DIFFRACTIONr_angle_other_deg0.949319932
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4451195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.21824.224438
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.073151467
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6291565
X-RAY DIFFRACTIONr_chiral_restr0.090.21433
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02110977
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022308
X-RAY DIFFRACTIONr_nbd_refined0.250.26642
X-RAY DIFFRACTIONr_nbd_other0.1640.217750
X-RAY DIFFRACTIONr_nbtor_refined0.1710.29166
X-RAY DIFFRACTIONr_nbtor_other0.0750.210144
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2806
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0060.24
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3040.2140
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2140.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1050.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6712.3074765
X-RAY DIFFRACTIONr_mcbond_other1.672.3064764
X-RAY DIFFRACTIONr_mcangle_it2.5833.4455953
X-RAY DIFFRACTIONr_mcangle_other2.5823.4465954
X-RAY DIFFRACTIONr_scbond_it1.8852.4874639
X-RAY DIFFRACTIONr_scbond_other1.8842.4874639
X-RAY DIFFRACTIONr_scangle_it3.0193.666829
X-RAY DIFFRACTIONr_scangle_other3.0193.666830
X-RAY DIFFRACTIONr_long_range_B_refined6.77619.54311867
X-RAY DIFFRACTIONr_long_range_B_other5.71418.52410856
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.121 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.219 349 -
Rwork0.199 17174 -
obs--99.89 %

+
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