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- PDB-1afs: RECOMBINANT RAT LIVER 3-ALPHA-HYDROXYSTEROID DEHYDROGENASE (3-ALP... -

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Basic information

Entry
Database: PDB / ID: 1afs
TitleRECOMBINANT RAT LIVER 3-ALPHA-HYDROXYSTEROID DEHYDROGENASE (3-ALPHA-HSD) COMPLEXED WITH NADP AND TESTOSTERONE
Components3-ALPHA-HYDROXYSTEROID DEHYDROGENASE
KeywordsOXIDOREDUCTASE / NAD
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / TESTOSTERONE / 3-alpha-hydroxysteroid dehydrogenase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBennett, M.J. / Albert, R.H. / Jez, J.M. / Ma, H. / Penning, T.M. / Lewis, M.
Citation
Journal: Structure / Year: 1997
Title: Steroid recognition and regulation of hormone action: crystal structure of testosterone and NADP+ bound to 3 alpha-hydroxysteroid/dihydrodiol dehydrogenase.
Authors: Bennett, M.J. / Albert, R.H. / Jez, J.M. / Ma, H. / Penning, T.M. / Lewis, M.
#1: 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.
#2: 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
DepositionMar 13, 1997Processing site: BNL
Revision 1.0Oct 8, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)76,4496
Polymers74,3852
Non-polymers2,0644
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-15 kcal/mol
Surface area25100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.400, 157.100, 49.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.956096, -0.220739, -0.192756), (-0.209149, -0.974704, 0.078799), (-0.205274, -0.035025, -0.978077)
Vector: 4.90967, 71.8141, -25.72155)

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Components

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


Mass: 37192.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: LIVER / Production host: unidentified (others)
References: UniProt: P23457, 3alpha-hydroxysteroid 3-dehydrogenase (Si-specific)
#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: Chemical ChemComp-TES / TESTOSTERONE


Mass: 288.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H28O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.66 %
Crystal growpH: 6.4 / Details: pH 6.4
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlternary complex1drop
220-21 %PEG80001reservoir
30.1 Msodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1996 / Details: SUPPER DOUBLE MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 26156 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 18
Reflection shellResolution: 2.5→2.7 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 4.3 / % possible all: 92.7
Reflection shell
*PLUS
% possible obs: 92.7 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LWI

1lwi


Resolution: 2.5→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.242 -10 %RANDOM
Rwork0.188 ---
obs0.188 25244 98.2 %-
Displacement parametersBiso mean: 28 Å2
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5162 0 138 58 5358
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
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
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.5→2.7 Å / Total num. of bins used: 6 /
Rfactor% reflection
Rfree0.317 10 %
Rwork0.257 -
obs-92.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3

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