2GGS | pdb_00002ggs

crystal structure of hypothetical dTDP-4-dehydrorhamnose reductase from sulfolobus tokodaii

• PDB DOI: https://doi.org/10.2210/pdb2GGS/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Sulfurisphaera tokodaii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-03-24 Released: 2007-03-24 
• Deposition Author(s): Rajakannan, V., Mizushima, T., Suzuki, A., Masui, R., Kuramitsu, S., Yamane, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.253 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

crystal structure of hypothetical dTDP-4-dehydrorhamnose reductase from sulfolobus tokodaii

Rajakannan, V., Mizushima, T., Suzuki, A., Masui, R., Kuramitsu, S., Yamane, T.

To be published.

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: 63.49 kDa 
• Atom Count: 4,995 
• Modelled Residue Count: 546 
• Deposited Residue Count: 546 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
273aa long hypothetical dTDP-4-dehydrorhamnose reductase	A, B	273	Sulfurisphaera tokodaii	Mutation(s): 0  EC: 1.1.1.133
UniProt
Find proteins for Q96Z61 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore Q96Z61  Go to UniProtKB:  Q96Z61

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	C [auth A], D [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.253 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.944	α = 90
b = 40.683	β = 116.18
c = 103.14	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-24 
Deposition Author(s): Rajakannan, V., Mizushima, T., Suzuki, A., Masui, R., Kuramitsu, S., Yamane, T.

Revision History  

• Version 1.0: 2007-03-24
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description