1SPX | pdb_00001spx

Crystal Structure of Glucose Dehydrogenase of Caenorhabditis Elegans in the Apo-Form

• PDB DOI: https://doi.org/10.2210/pdb1SPX/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Caenorhabditis elegans
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-03-17 Released: 2004-03-23 
• Deposition Author(s): Schormann, N., Zhou, J., McCombs, D., Bray, T., Symersky, J., Huang, W.-Y., Luan, C.-H., Gray, R., Luo, D., Arabashi, A., Bunzel, B., Nagy, L., Lu, S., Li, S., Lin, G., Zhang, Y., Qiu, S., Tsao, J., Luo, M., Carson, M., Southeast Collaboratory for Structural Genomics (SECSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.250 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Models: experimental

Literature

Crystal Structure of Glucose Dehydrogenase of Caenorhabditis Elegans in the Apo-Form: A Member of the SDR-Family

Schormann, N., Zhou, J., McCombs, D., Bray, T., Symersky, J., Huang, W.-Y., Luan, C.-H., Gray, R., Luo, D., Arabashi, A., Bunzel, B., Nagy, L., Lu, S., Li, S., Lin, G., Zhang, Y., Qiu, S., Tsao, J., Luo, M., Carson, M.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 29.4 kDa 
• Atom Count: 1,904 
• Modeled Residue Count: 237 
• Deposited Residue Count: 278 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
short-chain reductase family member (5L265)	A	278	Caenorhabditis elegans	Mutation(s): 0  Gene Names: D1054.8 EC: 1.1.1.47
UniProt
Find proteins for Q18946 (Caenorhabditis elegans) Explore Q18946  Go to UniProtKB:  Q18946

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.250 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.682	α = 90
b = 89.287	β = 90
c = 108.153	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-03-23 
Deposition Author(s): Schormann, N., Zhou, J., McCombs, D., Bray, T., Symersky, J., Huang, W.-Y., Luan, C.-H., Gray, R., Luo, D., Arabashi, A., Bunzel, B., Nagy, L., Lu, S., Li, S., Lin, G., Zhang, Y., Qiu, S., Tsao, J., Luo, M., Carson, M., Southeast Collaboratory for Structural Genomics (SECSG)

Revision History  

• Version 1.0: 2004-03-23
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Refinement description