1O51

Crystal structure of a putative PII-like signaling protein (TM0021) from Thermotoga maritima at 2.50 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1O51/pdb
• Entry: 1O51 supersedes: 1O2C

• Classification: SIGNALING PROTEIN
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-08-01 Released: 2003-08-19 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Literature

Crystal structure of a putative PII-like signaling protein (TM0021) from Thermotoga maritima at 2.5 A resolution

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

(2004) Proteins 54: 810-813

• PubMed: 14997579 
• DOI: https://doi.org/10.1002/prot.10647
• Primary Citation of Related Structures:  
  1O51

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Organizational Affiliation: 

Joint Center for Structural Genomics, La Jolla, CA 92037, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 14.04 kDa 
• Atom Count: 785 
• Modelled Residue Count: 89 
• Deposited Residue Count: 114 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein TM0021	A	114	Thermotoga maritima	Mutation(s): 3  Gene Names: TM0021
UniProt
Find proteins for Q9WXM9 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WXM9  Go to UniProtKB:  Q9WXM9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	D [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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: 2.50 Å
• R-Value Free:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M31O51

Space Group: P 4₃ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.11	α = 90
b = 100.11	β = 90
c = 100.11	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
RESOLVE	model building
SOLVE	phasing
REFMAC	refinement
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-08-19 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)
• This entry supersedes: 1O2C

Revision History  

• Version 1.0: 2003-08-19
  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: 2018-07-18
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.6: 2024-10-16
  Changes: Data collection, Structure summary