1XHL

Crystal Structure of putative Tropinone Reductase-II from Caenorhabditis Elegans with Cofactor and Substrate

• PDB DOI: https://doi.org/10.2210/pdb1XHL/pdb

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


• Deposited: 2004-09-20 Released: 2004-09-28 
• Deposition Author(s): Schormann, N., Karpova, E., Zhou, J., Zhang, Y., Symersky, J., Bunzel, R., 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: 2.40 Å
• R-Value Free: 0.215 
• R-Value Work: 0.191 
• R-Value Observed: 0.191 

Starting Models: experimental

Literature

Crystal Structure of putative Tropinone Reductase-II from Caenorhabditis Elegans with Cofactor and Substrate

Schormann, N., Karpova, E., Zhou, J., Zhang, Y., Symersky, J., Bunzel, R., 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,PQS (software)

Macromolecule Content

• Total Structure Weight: 64.88 kDa 
• Atom Count: 4,418 
• Modelled Residue Count: 548 
• Deposited Residue Count: 594 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Short-chain dehydrogenase/reductase family member (5L265), putative Tropinone Reductase-II	A, B	297	Caenorhabditis elegans	Mutation(s): 0  Gene Names: F25D1.5 EC: 1.1.1.236
UniProt
Find proteins for Q19774 (Caenorhabditis elegans) Explore Q19774  Go to UniProtKB:  Q19774

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	C [auth A], E [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
TNE	D [auth A], F [auth B]	8-METHYL-8-AZABICYCLO[3,2,1]OCTAN-3-ONE C8 H13 N O QQXLDOJGLXJCSE-KNVOCYPGSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.215 
• R-Value Work: 0.191 
• R-Value Observed: 0.191 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.589	α = 90
b = 109.589	β = 90
c = 162.591	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-09-28 
Deposition Author(s): Schormann, N., Karpova, E., Zhou, J., Zhang, Y., Symersky, J., Bunzel, R., 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: 2004-09-28
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description