3IX7 | pdb_00003ix7

Crystal structure of a domain of functionally unknown protein from Thermus thermophilus HB8

• PDB DOI: https://doi.org/10.2210/pdb3IX7/pdb

• Classification: Structural Genomics, Unknown function
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-09-03 Released: 2009-09-22 
• Deposition Author(s): Chang, C., Li, H., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.256 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Literature

Crystal structure of a domain of functionally unknown protein from Thermus thermophilus HB8

Chang, C., Li, H., Clancy, S., Joachimiak, A.

To be published.

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)

Macromolecule Content 

• Total Structure Weight: 29.59 kDa 
• Atom Count: 2,213 
• Modeled Residue Count: 261 
• Deposited Residue Count: 268 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein TTHA0540	A, B	134	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: TTHA0540 EC: 3.1
UniProt
Find proteins for Q5SKV3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SKV3  Go to UniProtKB:  Q5SKV3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACY	C [auth B]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.256 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.152	α = 90
b = 110.152	β = 90
c = 39.205	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	model building
RESOLVE	model building
Coot	model building
ARP/wARP	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-22 
Deposition Author(s): Chang, C., Li, H., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-09-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary