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- PDB-1lwi: 3-ALPHA-HYDROXYSTEROID/DIHYDRODIOL DEHYDROGENASE FROM RATTUS NORV... -

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Basic information

Entry
Database: PDB / ID: 1lwi
Title3-ALPHA-HYDROXYSTEROID/DIHYDRODIOL DEHYDROGENASE FROM RATTUS NORVEGICUS
Components3-ALPHA-HYDROXYSTEROID/DIHYDRODIOL DEHYDROGENASE
KeywordsOXIDOREDUCTASE / NAD
Function / homology
Function and homology information


3alpha-hydroxysteroid 3-dehydrogenase (Si-specific) / androsterone dehydrogenase (B-specific) activity / steroid dehydrogenase activity / androsterone dehydrogenase activity / ketosteroid monooxygenase activity / progesterone metabolic process / daunorubicin metabolic process / doxorubicin metabolic process / bile acid binding / aldose reductase (NADPH) activity ...3alpha-hydroxysteroid 3-dehydrogenase (Si-specific) / androsterone dehydrogenase (B-specific) activity / steroid dehydrogenase activity / androsterone dehydrogenase activity / ketosteroid monooxygenase activity / progesterone metabolic process / daunorubicin metabolic process / doxorubicin metabolic process / bile acid binding / aldose reductase (NADPH) activity / prostaglandin metabolic process / steroid metabolic process / hippocampus development / cytosol
Similarity search - Function
Aldo-keto reductase family 1 member C / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily ...Aldo-keto reductase family 1 member C / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 3-alpha-hydroxysteroid dehydrogenase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsBennett, M.J. / Schlegel, B.P. / Jez, J.M. / Penning, T.M. / Lewis, M.
Citation
Journal: Biochemistry / Year: 1996
Title: Structure of 3 alpha-hydroxysteroid/dihydrodiol dehydrogenase complexed with NADP+.
Authors: Bennett, M.J. / Schlegel, B.P. / Jez, J.M. / Penning, T.M. / Lewis, M.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Three-Dimensional Structure of Rat Liver 3 Alpha-Hydroxysteroid/Dihydrodiol Dehydrogenase: A Member of the Aldo-Keto Reductase Superfamily
Authors: Hoog, S.S. / Pawlowski, J.E. / Alzari, P.M. / Penning, T.M. / Lewis, M.
History
DepositionFeb 24, 1996Processing site: BNL
Revision 1.0Dec 7, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-ALPHA-HYDROXYSTEROID/DIHYDRODIOL DEHYDROGENASE
B: 3-ALPHA-HYDROXYSTEROID/DIHYDRODIOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,6444
Polymers74,1572
Non-polymers1,4872
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-17 kcal/mol
Surface area26030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.900, 139.100, 53.300
Angle α, β, γ (deg.)90.00, 113.50, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.999953, -0.003338, -0.009108), (-0.002902, -0.998871, 0.047415), (-0.009256, -0.047386, -0.998834)
Vector: 0.1352, -76.8019, 97.3784)

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Components

#1: Protein 3-ALPHA-HYDROXYSTEROID/DIHYDRODIOL DEHYDROGENASE


Mass: 37078.547 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: FORMERLY EC 1.1.1.50, HOWEVER A NEW CONVENTION DISTINGUISHES THIS AS AN A CLASS DEHYDROGENASE
Source: (natural) Rattus norvegicus (Norway rat) / Organ: LIVER / Strain: SPRAGUE-DAWLEY / References: UniProt: P23457, EC: 1.1.1.213
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 40 %
Crystal grow
*PLUS
pH: 5.7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlbinary complex1drop
227 %(w/v)PEG40001reservoir
30.19 Mammonium acetate1reservoir
40.10 Msodium acetate1reservoir
51.3 %(v/v)dimethyl sulfoxide1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 16123 / % possible obs: 90 % / Redundancy: 3 % / Rmerge(I) obs: 0.058
Reflection
*PLUS
Num. all: 17221 / Num. measured all: 53539

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMdata reduction
CCP4data reduction
X-PLOR3.1phasing
RefinementResolution: 2.7→5 Å
RfactorNum. reflection
Rfree0.294 -
Rwork0.234 -
obs0.234 12308
Displacement parametersBiso mean: 29 Å2
Refinement stepCycle: LAST / Resolution: 2.7→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4906 0 192 2 5100
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.5
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.5

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