2B8N

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.53 Å
R-Value Free: 0.246
R-Value Work: 0.182
R-Value Observed: 0.185

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

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

Organizational Affiliation

Joint Center for Structural Genomics.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9X1S1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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
R-Value Work: 0.182
R-Value Observed: 0.185
Space Group: P 2₁ 2₁ 2₁
Diffraction Data: https://doi.org/10.18430/M32B8N

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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2005-11-08

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

This entry supersedes: 1O0U

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.