2AFB

Crystal structure of 2-dehydro-3- deoxygluconokinase (EC 2.7.1.45) (tm0067) from THERMOTOGA MARITIMA at 2.05 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2AFB/pdb
• Entry: 2AFB supersedes: 1J5V

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


• Deposited: 2005-07-25 Released: 2006-02-14 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.230 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 

Literature

Crystal structure of 2-keto-3-deoxygluconate kinase (TM0067) from Thermotoga maritima at 2.05 A resolution.

Mathews, I.I., McMullan, D., 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., Rife, C.L., Schwarzenbacher, R., Spraggon, G., Stevens, R.C., van den Bedem, H., Weekes, D., Wolf, G., Hodgson, K.O., Wooley, J., Deacon, A.M., Godzik, A., Lesley, S.A., Wilson, I.A.

(2007) Proteins 70: 603-608

• PubMed: 18004772 
• DOI: https://doi.org/10.1002/prot.21842
• Primary Citation of Related Structures:  
  2AFB

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Organizational Affiliation: 

Stanford Synchrotron Radiation Laboratory, Stanford University, Menlo Park, California, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 79.48 kDa 
• Atom Count: 5,444 
• Modelled Residue Count: 655 
• Deposited Residue Count: 702 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-keto-3-deoxygluconate kinase	A, B	351	Thermotoga maritima MSB8	Mutation(s): 8  Gene Names: tm0067
UniProt
Find proteins for Q9WXS2 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WXS2  Go to UniProtKB:  Q9WXS2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	C [auth A], D [auth A], E [auth A], H [auth B], I [auth B], J [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
CA	F [auth A], G [auth A], K [auth B], L [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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: 2.05 Å
• R-Value Free: 0.230 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 
• Space Group: H 3 2
• Diffraction Data: https://doi.org/10.18430/M32AFB

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.993	α = 90
b = 120.993	β = 90
c = 260.3	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-02-14 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)
• This entry supersedes: 1J5V

Revision History  

• Version 1.0: 2006-02-14
  Type: Initial release
  
• Version 1.1: 2007-12-26
  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: 2024-10-16
  Changes: Data collection, Refinement description, Structure summary