Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 12.39 kDa 
• Atom Count: 1049 
• Modelled Residue Count: 82 
• Deposited Residue Count: 82 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

1XYI

Hyperthermophile chromosomal protein Sac7d double mutant Val26Ala/Met29Ala in complex with DNA GCGATCGC

• PDB DOI: 10.2210/pdb1XYI/pdb
• NDB: PD0607

• Classification: STRUCTURAL PROTEIN/DNA
• Organism(s): Sulfolobus acidocaldarius
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-11-10 Released: 2005-02-08 
• Deposition Author(s): Chen, C.-Y., Ko, T.-P., Lin, T.-W., Chou, C.-C., Chen, C.-J., Wang, A.H.-J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.255 
• R-Value Work: 0.214 
• R-Value Observed: 0.216 

Literature

Probing the DNA kink structure induced by the hyperthermophilic chromosomal protein Sac7d

Chen, C.-Y., Ko, T.-P., Lin, T.-W., Chou, C.-C., Chen, C.-J., Wang, A.H.-J.

(2005) Nucleic Acids Res 33: 430-438

• PubMed: 15653643 
• DOI: 10.1093/nar/gki191
• Primary Citation of Related Structures:  
  1WTO, 1WTP, 1WTQ, 1WTR, 1WTV, 1WTW, 1WTX, 1XYI


• PubMed Abstract: 
  

Sac7d, a small, abundant, sequence-general DNA-binding protein from the hyperthermophilic archaeon Sulfolobus acidocaldarius, causes a single-step sharp kink in DNA (approximately 60 degrees) via the intercalation of both Val26 and Met29. These two amino acids were systematically changed in size to probe their effects on DNA kinking. Eight crystal structures of five Sac7d mutant-DNA complexes have been analyzed. The DNA-binding pattern of the V26A and M29A single mutants is similar to that of the wild-type, whereas the V26A/M29A protein binds DNA without side chain intercalation, resulting in a smaller overall bending (approximately 50 degrees). The M29F mutant inserts the Phe29 side chain orthogonally to the C2pG3 step without stacking with base pairs, inducing a sharp kink (approximately 80 degrees). In the V26F/M29F-GCGATCGC complex, Phe26 intercalates deeply into DNA bases by stacking with the G3 base, whereas Phe29 is stacked on the G15 deoxyribose, in a way similar to those used by the TATA box-binding proteins. All mutants have reduced DNA-stabilizing ability, as indicated by their lower T m values. The DNA kink patterns caused by different combinations of hydrophobic side chains may be relevant in understanding the manner by which other minor groove-binding proteins interact with DNA.

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Organizational Affiliation: 

Institute of Biological Chemistry Taipei 115, Taiwan.

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-binding proteins 7a/7b/7d	C [auth A]	66	Sulfolobus acidocaldarius	Mutation(s): 2  Gene Names: sac7d
UniProt
Find proteins for P13123 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770)) Explore P13123  Go to UniProtKB:  P13123

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3'	A [auth B], B [auth C]	8	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.255 
• R-Value Work: 0.214 
• R-Value Observed: 0.216 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.78	α = 90
b = 47.27	β = 90
c = 52.65	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-11-10 
• Released Date: 2005-02-08 
Deposition Author(s): Chen, C.-Y., Ko, T.-P., Lin, T.-W., Chou, C.-C., Chen, C.-J., Wang, A.H.-J.

Revision History  

• Version 1.0: 2005-02-08
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-10
  Changes: Advisory, Database references