3LN3 | pdb_00003ln3

Crystal structure of Putative reductase (NP_038806.2) from MUS MUSCULUS at 1.18 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3LN3/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-02-01 Released: 2010-02-16 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.18 Å
• R-Value Free: 
  0.156 (Depositor), 0.164 (DCC) 
• R-Value Work: 
  0.131 (Depositor), 0.142 (DCC) 
• R-Value Observed: 
  0.132 (Depositor) 

Literature

Crystal structure of Putative reductase (NP_038806.2) from MUS MUSCULUS at 1.18 A resolution

Joint Center for Structural Genomics (JCSG)

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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 39.24 kDa 
• Atom Count: 3,271 
• Modeled Residue Count: 319 
• Deposited Residue Count: 324 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrodiol dehydrogenase	A	324	Mus musculus	Mutation(s): 0  Gene Names: Akr1c13, ddh EC: 1.1.1
UniProt
Find proteins for Q8VC28 (Mus musculus) Explore Q8VC28  Go to UniProtKB:  Q8VC28

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
MRD	F [auth A]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N
SO4	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY	A	L-PEPTIDE LINKING	C8 H18 N2 O2		LYS
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.18 Å
• R-Value Free:  0.156 (Depositor), 0.164 (DCC) 
• R-Value Work:  0.131 (Depositor), 0.142 (DCC) 
• R-Value Observed: 0.132 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33LN3

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.506	α = 90
b = 47.206	β = 94.98
c = 47.1	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-16 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2010-02-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary