2DT5 | pdb_00002dt5

Crystal Structure of TTHA1657 (AT-rich DNA-binding protein) from Thermus thermophilus HB8

• PDB DOI: https://doi.org/10.2210/pdb2DT5/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-07-11 Released: 2007-01-02 
• Deposition Author(s): Nakamura, A., Sosa, A., Komori, H., Kita, A., Miki, K., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free: 
  0.238 (Depositor) 
• R-Value Work: 
  0.195 (Depositor) 
• R-Value Observed: 
  0.195 (Depositor) 

Literature

Crystal structure of TTHA1657 (AT-rich DNA-binding protein; p25) from Thermus thermophilus HB8 at 2.16 A resolution

Nakamura, A., Sosa, A., Komori, H., Kita, A., Miki, K.

(2007) Proteins 66: 755-759

• PubMed: 17154156 
• DOI: https://doi.org/10.1002/prot.21222
• Primary Citation Related Structures: 
  2DT5

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Organizational Affiliation: 
• Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 48.39 kDa 
• Atom Count: 3,667 
• Modeled Residue Count: 421 
• Deposited Residue Count: 422 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AT-rich DNA-binding protein	A, B	211	Thermus thermophilus HB8	Mutation(s): 1  Gene Names: TTHA1657
UniProt
Find proteins for Q5SHS3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHS3  Go to UniProtKB:  Q5SHS3

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	H [auth A], L [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
SO4	C [auth A], D [auth A], E [auth A], F [auth A], J [auth B], K [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	I [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free:  0.238 (Depositor) 
• R-Value Work:  0.195 (Depositor) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.595	α = 90
b = 135.595	β = 90
c = 68.424	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-01-02 
Deposition Author(s): Nakamura, A., Sosa, A., Komori, H., Kita, A., Miki, K., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-01-02
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.4: 2024-05-29
  Changes: Data collection