1VK9 | pdb_00001vk9

CRYSTAL STRUCTURE OF A DUF1893 family protein (TM1506) FROM THERMOTOGA MARITIMA AT 2.70 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb1VK9/pdb

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


• Deposited: 2004-05-06 Released: 2004-05-18 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.251 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Literature

Crystal structure of an ADP-ribosylated protein with a cytidine deaminase-like fold, but unknown function (TM1506), from Thermotoga maritima at 2.70 A resolution.

Xu, Q., Kozbial, P., McMullan, D., Krishna, S.S., Brittain, S.M., Ficarro, S.B., DiDonato, M., Miller, M.D., Abdubek, P., Axelrod, H.L., Chiu, H.J., Clayton, T., Duan, L., Elsliger, M.A., Feuerhelm, J., Grzechnik, S.K., Hale, J., Han, G.W., Jaroszewski, L., Klock, H.E., Morse, A.T., Nigoghossian, E., Paulsen, J., Reyes, R., Rife, C.L., van den Bedem, H., White, A., Hodgson, K.O., Wooley, J., Deacon, A.M., Godzik, A., Lesley, S.A., Wilson, I.A.

(2008) Proteins 71: 1546-1552

• PubMed: 18275082 
• DOI: https://doi.org/10.1002/prot.21992
• Primary Citation Related Structures: 
  1VK9

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Organizational Affiliation: 
• Joint Center for Structural Genomics, Menlo Park, California, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 17.83 kDa 
• Atom Count: 1,195 
• Modeled Residue Count: 147 
• Deposited Residue Count: 151 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
conserved hypothetical protein TM1506	A	151	Thermotoga maritima	Mutation(s): 5  Gene Names: TM1506
UniProt
Find proteins for Q9X1J4 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X1J4  Go to UniProtKB:  Q9X1J4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
UNL	H [auth A]	Unknown ligand PTFCDOFLOPIGGS-UHFFFAOYSA-N

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: 2.70 Å
• R-Value Free:  0.251 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M31VK9

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.891	α = 90
b = 132.891	β = 90
c = 66.379	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHELXD	phasing
autoSHARP	phasing
SOLOMON	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-05-18 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2004-05-18
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-20
  Changes: Data collection, Structure summary