1O3U | pdb_00001o3u

Crystal structure of an hepn domain protein (tm0613) from thermotoga maritima at 1.75 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1O3U/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-03-28 Released: 2003-04-22 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.237 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Literature

Crystal structure of an HEPN domain protein (TM0613) from Thermotoga maritima at 1.75 A resolution.

Erlandsen, H., Canaves, J.M., Elsliger, M.A., von Delft, F., Brinen, L.S., Dai, X., Deacon, A.M., Floyd, R., Godzik, A., Grittini, C., Grzechnik, S.K., Jaroszewski, L., Klock, H.E., Koesema, E., Kovarik, J.S., Kreusch, A., Kuhn, P., Lesley, S.A., McMullan, D., McPhillips, T.M., Miller, M.D., Morse, A., Moy, K., Ouyang, J., Page, R., Robb, A., Quijano, K., Schwarzenbacher, R., Spraggon, G., Stevens, R.C., van den Bedem, H., Velasquez, J., Vincent, J., Wang, X., West, B., Wolf, G., Hodgson, K.O., Wooley, J., Wilson, I.A.

(2004) Proteins 54: 806-809

• PubMed: 14997578 
• DOI: https://doi.org/10.1002/prot.10631
• Primary Citation Related Structures: 
  1O3U

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Organizational Affiliation: 
• The Scripps Research Institute, La Jolla, California 92037, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 15.62 kDa 
• Atom Count: 1,096 
• Modeled Residue Count: 120 
• Deposited Residue Count: 135 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
conserved hypothetical protein TM0613	A	135	Thermotoga maritima	Mutation(s): 1  Gene Names: TM0613
UniProt
Find proteins for Q9WZ82 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WZ82  Go to UniProtKB:  Q9WZ82

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.237 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M31O3U

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.922	α = 90
b = 57.922	β = 90
c = 63.735	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
RESOLVE	model building
SOLVE	phasing
REFMAC	refinement
CCP4	data scaling
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-04-22 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2003-04-22
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2018-07-18
  Changes: Data collection, Database references
• Version 1.5: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.6: 2024-10-30
  Changes: Data collection, Structure summary