1ANV | pdb_00001anv

ADENOVIRUS 5 DBP/URANYL FLUORIDE SOAK

• PDB DOI: https://doi.org/10.2210/pdb1ANV/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Human adenovirus 5
• Mutation(s): No 


• Deposited: 1996-03-14 Released: 1997-02-12 
• Deposition Author(s): Kanellopoulos, P.N., Tsernoglou, D., Van Der Vliet, P.C., Tucker, P.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.310 (Depositor) 
• R-Value Work: 
  0.204 (Depositor), 0.190 (DCC) 

Starting Model: experimental

Literature

Conformational change of the adenovirus DNA-binding protein induced by soaking crystals with K3UO2F5 solutions.

Kanellopoulos, P.N., Tsernoglou, D., van der Vliet, P.C., Tucker, P.A.

(1996) Acta Crystallogr D Biol Crystallogr 52: 942-945

• PubMed: 15299602 
• DOI: https://doi.org/10.1107/S0907444996005525
• Primary Citation of Related Structures:  
  1ANV


• PubMed Abstract: 
  

  Soaking crystals of the C-terminal DNA-binding domain of the adenovirus single-stranded DNA-binding protein with a buffer containing K(3)UO(2)F(5) results in a 9% change of the crystallographic c axis without destruction of the crystals or appreciable loss of resolution. The crystals belong to space group P2(1)2(1)2(1) with a = 79.7, b = 75.6 and c = 60.6 A. The three-dimensional structure has been refined to 2.7 A with a crystallographic R factor of 0.206. Antiparallel chains of protein molecules running through the entire crystal are linked by uranyl ions. The relative orientation of protein monomers is flexible, even in the crystalline state, and allows changes in the packing of the protein chains.

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Organizational Affiliation: 

Structural Biology Programme, European Molecular Biology Laboratory, Heidelberg, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 41.11 kDa 
• Atom Count: 2,500 
• Modeled Residue Count: 314 
• Deposited Residue Count: 356 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADENOVIRUS SINGLE-STRANDED DNA-BINDING PROTEIN	A	356	Human adenovirus 5	Mutation(s): 0
UniProt
Find proteins for P03265 (Human adenovirus C serotype 5) Explore P03265  Go to UniProtKB:  P03265

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IUM	D [auth A], E [auth A], F [auth A], G [auth A]	URANYL (VI) ION O2 U IZLHQJIUOZHTLW-UHFFFAOYSA-N
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.310 (Depositor) 
• R-Value Work:  0.204 (Depositor), 0.190 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.7	α = 90
b = 75.6	β = 90
c = 60.6	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
TNT	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-02-12 
Deposition Author(s): Kanellopoulos, P.N., Tsernoglou, D., Van Der Vliet, P.C., Tucker, P.A.

Revision History  

• Version 1.0: 1997-02-12
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-04-04
  Changes: Data collection, Structure summary
• Version 1.4: 2023-08-02
  Changes: Database references, Derived calculations, Refinement description
• Version 1.5: 2024-05-22
  Changes: Data collection