2AX3 | pdb_00002ax3

CRYSTAL STRUCTURE OF A PUTATIVE CARBOHYDRATE KINASE (TM0922) FROM THERMOTOGA MARITIMA MSB8 AT 2.25 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb2AX3/pdb

• Classification: TRANSFERASE
• Organism(s): Thermotoga maritima MSB8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-09-02 Released: 2005-10-04 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.170 (DCC) 

Literature

Crystal structure of hypothetical protein (tm0922) from THERMOTOGA MARITIMA at 2.27 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Hetero 16-mer - A8B8 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 16-mer - A8B1C1D1E1F1G1H1I1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 55.91 kDa 
• Atom Count: 3,889 
• Modeled Residue Count: 499 
• Deposited Residue Count: 510 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein TM0922	A	502	Thermotoga maritima MSB8	Mutation(s): 0  Gene Names: tm0922 EC: 4.2.1.136 (UniProt), 5.1.99.6 (UniProt)
UniProt
Find proteins for Q9X024 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X024  Go to UniProtKB:  Q9X024

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
unknown peptide	B	8	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-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: 2.27 Å
• R-Value Free:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.170 (DCC) 

Diffraction Data: https://doi.org/10.18430/M32AX3

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.264	α = 90
b = 121.264	β = 90
c = 153.873	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-10-04 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2005-10-04
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-06
  Changes: Data collection, Structure summary