2B8N | pdb_00002b8n

Crystal structure of Glycerate kinase (EC 2.7.1.31) (tm1585) from THERMOTOGA MARITIMA at 2.70 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2B8N/pdb
• Entry: 2B8N supersedes: 1O0U

• Classification: TRANSFERASE
• Organism(s): Thermotoga maritima MSB8
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-10-07 Released: 2005-11-08 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.53 Å
• R-Value Free: 
  0.246 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Literature

Crystal structure of a glycerate kinase (TM1585) from Thermotoga maritima at 2.70 A resolution reveals a new fold

Schwarzenbacher, R., McMullan, D., Krishna, S.S., Xu, Q., Miller, M.D., Canaves, J.M., Elsliger, M.A., Floyd, R., Grzechnik, S.K., Jaroszewski, L., Klock, H.E., Koesema, E., Kovarik, J.S., Kreusch, A., Kuhn, P., McPhillips, T.M., Morse, A.T., Quijano, K., Spraggon, G., Stevens, R.C., van den Bedem, H., Wolf, G., Hodgson, K.O., Wooley, J., Deacon, A.M., Godzik, A., Lesley, S.A., Wilson, I.A.

(2006) Proteins 65: 243-248

• PubMed: 16865707 
• DOI: https://doi.org/10.1002/prot.21058
• Primary Citation of Related Structures:  
  2B8N

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Organizational Affiliation: 
• Joint Center for Structural Genomics.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 92.95 kDa 
• Atom Count: 6,244 
• Modeled Residue Count: 828 
• Deposited Residue Count: 858 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
glycerate kinase, putative	A, B	429	Thermotoga maritima MSB8	Mutation(s): 5  Gene Names: tm1585 EC: 2.7.1.31 (PDB Primary Data), 2.7.1.165 (UniProt)
UniProt
Find proteins for Q9X1S1 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X1S1  Go to UniProtKB:  Q9X1S1

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.53 Å
• R-Value Free:  0.246 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32B8N

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.954	α = 90
b = 85.169	β = 90
c = 172.507	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELX	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-11-08 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)
• This entry supersedes: 1O0U

Revision History  

• Version 1.0: 2005-11-08
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.3: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.4: 2024-10-30
  Changes: Data collection, Refinement description, Structure summary