1XKQ | pdb_00001xkq

Crystal Structure of Short-Chain Dehydrogenase/Reductase of unknown Function from Caenorhabditis Elegans with Cofactor

• PDB DOI: https://doi.org/10.2210/pdb1XKQ/pdb

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


• Deposited: 2004-09-29 Released: 2004-10-12 
• Deposition Author(s): Schormann, N., Zhou, J., Karpova, E., Zhang, Y., Symersky, J., Bunzel, B., Huang, W.-Y., Arabshahi, A., Qiu, S., Luan, C.-H., Gray, R., Carson, M., Tsao, J., Luo, M., Johnson, D., Lu, S., Lin, G., Luo, D., Cao, Z., Li, S., McKinstry, A., Shang, Q., Chen, Y.-J., Bray, T., Nagy, L., DeLucas, L., Southeast Collaboratory for Structural Genomics (SECSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.245 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Models: experimental

Literature

Crystal Structure of Short-Chain Dehydrogenase/Reductase of unknown Function from Caenorhabditis Elegans with Cofactor

Schormann, N., Zhou, J., Karpova, E., Zhang, Y., Symersky, J., Bunzel, B., Huang, W.-Y., Arabshahi, A., Qiu, S., Luan, C.-H., Gray, R., Carson, M., Tsao, J., Luo, M., Johnson, D., Lu, S., Lin, G., Luo, D., Cao, Z., Li, S., McKinstry, A., Shang, Q., Chen, Y.-J., Bray, T., Nagy, L., DeLucas, L.

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 (software)

Macromolecule Content 

• Total Structure Weight: 122.79 kDa 
• Atom Count: 8,955 
• Modeled Residue Count: 1,085 
• Deposited Residue Count: 1,120 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
short-chain reductase family member (5D234)	A, B, C, D	280	Caenorhabditis elegans	Mutation(s): 0  Gene Names: R05D8.7
UniProt
Find proteins for Q9N5G4 (Caenorhabditis elegans) Explore Q9N5G4  Go to UniProtKB:  Q9N5G4

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.245 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.69	α = 90
b = 119.69	β = 90
c = 193.22	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-10-12 
Deposition Author(s): Schormann, N., Zhou, J., Karpova, E., Zhang, Y., Symersky, J., Bunzel, B., Huang, W.-Y., Arabshahi, A., Qiu, S., Luan, C.-H., Gray, R., Carson, M., Tsao, J., Luo, M., Johnson, D., Lu, S., Lin, G., Luo, D., Cao, Z., Li, S., McKinstry, A., Shang, Q., Chen, Y.-J., Bray, T., Nagy, L., DeLucas, L., Southeast Collaboratory for Structural Genomics (SECSG)

Revision History  

• Version 1.0: 2004-10-12
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description