5NXF

Crystal structure of the carboxy-terminal region of the bacteriophage T4 proximal long tail fibre protein gp34, residues 795 to 1289, at 1.9 Angstrom.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history. 


Literature

Crystal Structure of the Carboxy-Terminal Region of the Bacteriophage T4 Proximal Long Tail Fiber Protein Gp34.

Granell, M., Namura, M., Alvira, S., Kanamaru, S., van Raaij, M.J.

(2017) Viruses 9

  • DOI: https://doi.org/10.3390/v9070168
  • Primary Citation of Related Structures:  
    4UXE, 4UXF, 4UXG, 5NXF, 5NXH

  • PubMed Abstract: 

    Long tail fibers of bacteriophage T4 are formed by proteins gp34, gp35, gp36, and gp37, with gp34 located at the phage-proximal end and gp37 at the phage-distal, receptor-binding end. We have solved the structure of the carboxy-terminal region of gp34, consisting of amino acids 894-1289, by single-wavelength anomalous diffraction and extended the structure to amino acids 744-1289 using data collected from crystals containing longer gp34-fragments. The structure reveals three repeats of a mixed α-β fibrous domain in residues 744 to 877. A triple-helical neck connects to an extended triple β-helix domain (amino acids 900-1127) punctuated by two β-prism domains. Next, a β-prism domain decorated with short helices and extended β-helices is present (residues 1146-1238), while the C -terminal end is capped with another short β-helical region and three β-hairpins. The structure provides insight into the stability of the fibrous gp34 protein.

    • Organizational Affiliation: 

    Departmento de Estructura de Macromoleculas, Centro Nacional de Biotecnologia (CNB-CSIC), Calle Darwin 3, E-28049 Madrid, Spain.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Long-tail fiber proximal subunit
A, B, C
509Tequatrovirus T4Mutation(s): 0 
Gene Names: 34
UniProt
Find proteins for P18771 (Enterobacteria phage T4)
Explore P18771 
Go to UniProtKB:  P18771
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18771
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4
Download Ideal Coordinates CCD File 
G [auth A],
P [auth B],
Z [auth C]		PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL
Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
K [auth B]
L [auth B]
D [auth A],
E [auth A],
F [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
Q [auth C],
R [auth C],
S [auth C],
T [auth C],
U [auth C],
V [auth C],
W [auth C],
X [auth C],
Y [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
URE
Query on URE
Download Ideal Coordinates CCD File 
AA [auth C]UREA
C H4 N2 O
XSQUKJJJFZCRTK-UHFFFAOYSA-N
ACT
Query on ACT
Download Ideal Coordinates CCD File 
H [auth A],
I [auth A]		ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA
Query on NA
Download Ideal Coordinates CCD File 
J [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.107α = 90
b = 75.943β = 90.21
c = 149.128γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpainBFU2008-01588
Spanish Ministry of Economy and CompetitivenessBFU2011-24843
Spanish Ministry of Economy and CompetitivenessBFU2014-53425-P
Spanish Ministry of Economy and CompetitivenessSpainBFU2014-61367-EXP
European CommissionSpainNMP4-CT-2006-033256
Japan Society for the Promotion of ScienceJapanJP25440066

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-12
    Type: Initial release
  • Version 1.1: 2017-07-19
    Changes: Database references
  • Version 2.0: 2017-09-13
    Changes: Atomic model, Author supporting evidence, Derived calculations, Structure summary
  • Version 2.1: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description