3KBB

Crystal structure of putative beta-phosphoglucomutase from Thermotoga maritima

• PDB DOI: https://doi.org/10.2210/pdb3KBB/pdb
• Entry: 3KBB supersedes: 2PIB

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


• Deposited: 2009-10-20 Released: 2009-11-17 
• Deposition Author(s): Strange, R.W., Antonyuk, S.V., Ellis, M.J., Bessho, Y., Kuramitsu, S., Yokoyama, S., Hasnain, S.S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 0.238 
• R-Value Work: 0.191 
• R-Value Observed: 0.194 

Literature

Structure of a putative beta-phosphoglucomutase (TM1254) from Thermotoga maritima.

Strange, R.W., Antonyuk, S.V., Ellis, M.J., Bessho, Y., Kuramitsu, S., Shinkai, A., Yokoyama, S., Hasnain, S.S.

(2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 1218-1221

• PubMed: 20054115 
• DOI: https://doi.org/10.1107/S1744309109046302
• Primary Citation of Related Structures:  
  3KBB


• PubMed Abstract: 
  

  The structure of TM1254, a putative beta-phosphoglucomutase from T. maritima, was determined to 1.74 A resolution in a high-throughput structural genomics programme. Diffraction data were obtained from crystals belonging to space group P22(1)2(1), with unit-cell parameters a = 48.16, b = 66.70, c = 83.80 A, and were refined to an R factor of 19.2%. The asymmetric unit contained one protein molecule which is comprised of two domains. Structural homologues were found from protein databases that confirmed a strong resemblance between TM1254 and members of the haloacid dehalogenase (HAD) hydrolase family.

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Organizational Affiliation: 

Molecular Biophysics Group, School of Biological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, England. [e-mail]

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 25.7 kDa 
• Atom Count: 2,048 
• Modelled Residue Count: 216 
• Deposited Residue Count: 216 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphorylated carbohydrates phosphatase TM_1254	A	216	Thermotoga maritima MSB8	Mutation(s): 0  Gene Names: bpgm, tm_1254 EC: 3.1.3
UniProt
Find proteins for Q9X0Y1 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X0Y1  Go to UniProtKB:  Q9X0Y1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth A], G [auth A], H [auth A], I [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: 1.74 Å
• R-Value Free: 0.238 
• R-Value Work: 0.191 
• R-Value Observed: 0.194 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.16	α = 90
b = 66.698	β = 90
c = 83.8	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-17 
Deposition Author(s): Strange, R.W., Antonyuk, S.V., Ellis, M.J., Bessho, Y., Kuramitsu, S., Yokoyama, S., Hasnain, S.S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
• This entry supersedes: 2PIB

Revision History  

• Version 1.0: 2009-11-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary