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- PDB-1ral: THREE-DIMENSIONAL STRUCTURE OF RAT LIVER 3ALPHA-HYDROXYSTEROID(SL... -

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Basic information

Entry
Database: PDB / ID: 1ral
TitleTHREE-DIMENSIONAL STRUCTURE OF RAT LIVER 3ALPHA-HYDROXYSTEROID(SLASH)DIHYDRODIOL DEHYDROGENASE: A MEMBER OF THE ALDO-KETO REDUCTASE SUPERFAMILY
Components3-ALPHA-HYDROXYSTEROID DEHYDROGENASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


3alpha-hydroxysteroid 3-dehydrogenase (Si-specific) / : / steroid dehydrogenase activity / androsterone dehydrogenase [NAD(P)+] activity / ketosteroid monooxygenase activity / progesterone metabolic process / bile acid binding / daunorubicin metabolic process / doxorubicin metabolic process / aldose reductase (NADPH) activity ...3alpha-hydroxysteroid 3-dehydrogenase (Si-specific) / : / steroid dehydrogenase activity / androsterone dehydrogenase [NAD(P)+] activity / ketosteroid monooxygenase activity / progesterone metabolic process / bile acid binding / daunorubicin metabolic process / doxorubicin metabolic process / 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
3-alpha-hydroxysteroid dehydrogenase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsHoog, S.S. / Pawlowski, J.E. / Alzari, P.M. / Penning, T.M. / Lewis, M.
CitationJournal: 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 4, 1994Processing site: BNL
Revision 1.0Apr 30, 1994Provider: 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 / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-ALPHA-HYDROXYSTEROID DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)35,3321
Polymers35,3321
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.300, 89.500, 143.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Atom site foot note1: SER 232 - PRO 233 OMEGA =218.95 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: THR 251 - PRO 252 OMEGA =212.66 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

#1: Protein 3-ALPHA-HYDROXYSTEROID DEHYDROGENASE


Mass: 35331.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat)
References: UniProt: P23457, 3alpha-hydroxysteroid 3-dehydrogenase (Si-specific)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.14 %
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 5.8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 %(w/v)PEG60001reservoir
2100 mMsodium citrate1reservoir
3120 mMammonium sulfate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 10 Å / Num. obs: 6122 / % possible obs: 96 % / Num. measured all: 30872 / Rmerge(I) obs: 0.098

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 3→10 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.22 -
obs0.22 5883
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3029 0 0 0 3029
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
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_deg3.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Highest resolution: 3 Å / Lowest resolution: 10 Å / Num. reflection obs: 5883 / σ(F): 1 / Rfactor obs: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 17 Å2
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.8

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