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- PDB-3dop: Crystal structure of 5beta-reductase (AKR1D1) in complex with NAD... -

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Basic information

Entry
Database: PDB / ID: 3dop
TitleCrystal structure of 5beta-reductase (AKR1D1) in complex with NADP+ and 5beta-dihydrotestosterone, Resolution 2.00A
Components3-oxo-5-beta-steroid 4-dehydrogenase
KeywordsOXIDOREDUCTASE / PRODUCT / Bile acid catabolism / Cytoplasm / Disease mutation / Intrahepatic cholestasis / Lipid metabolism / NADP / Steroid metabolism
Function / homology
Function and homology information


Delta4-3-oxosteroid 5beta-reductase / C21-steroid hormone metabolic process / steroid dehydrogenase activity / bile acid catabolic process / delta4-3-oxosteroid 5beta-reductase activity / bile acid biosynthetic process / ketosteroid monooxygenase activity / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / aldo-keto reductase (NADPH) activity / cholesterol catabolic process ...Delta4-3-oxosteroid 5beta-reductase / C21-steroid hormone metabolic process / steroid dehydrogenase activity / bile acid catabolic process / delta4-3-oxosteroid 5beta-reductase activity / bile acid biosynthetic process / ketosteroid monooxygenase activity / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / aldo-keto reductase (NADPH) activity / cholesterol catabolic process / aldose reductase (NADPH) activity / androgen metabolic process / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / digestion / steroid binding / cytosol
Similarity search - Function
Aldo-keto reductase family 1 member D1 / 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 D1 / 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
5-beta-DIHYDROTESTOSTERONE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aldo-keto reductase family 1 member D1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsDi Costanzo, L. / Drury, J.E. / Penning, T.M. / Christianson, D.W.
CitationJournal: Mol.Cell.Endocrinol. / Year: 2009
Title: Structure and catalytic mechanism of human steroid 5beta-reductase (AKR1D1)
Authors: Di Costanzo, L. / Drury, J.E. / Christianson, D.W. / Penning, T.M.
History
DepositionJul 5, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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-oxo-5-beta-steroid 4-dehydrogenase
B: 3-oxo-5-beta-steroid 4-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9765
Polymers79,1992
Non-polymers1,7773
Water10,593588
1
A: 3-oxo-5-beta-steroid 4-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3432
Polymers39,5991
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 3-oxo-5-beta-steroid 4-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6333
Polymers39,5991
Non-polymers1,0342
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.872, 109.495, 129.199
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 3-oxo-5-beta-steroid 4-dehydrogenase / Delta(4)-3-ketosteroid 5-beta-reductase / Aldo-keto reductase family 1 member D1


Mass: 39599.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1D1, SRD5B1 / Plasmid: PET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Ecol
References: UniProt: P51857, Delta4-3-oxosteroid 5beta-reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-BDT / 5-beta-DIHYDROTESTOSTERONE / (5beta,8alpha,17beta)-17-hydroxyandrostan-3-one


Mass: 290.440 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H30O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 588 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsON THE ACTIVE SITE OF MONOMER A AN INTERPRETABLE PEAK CORRESPONDING TO THE BINDING SITE OF 5-BETA- ...ON THE ACTIVE SITE OF MONOMER A AN INTERPRETABLE PEAK CORRESPONDING TO THE BINDING SITE OF 5-BETA-DIHYDROTESTOSTERONE WAS OBSERVED AND IT IS MISSING FROM THE MODEL.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: ISOPROPANOL, PEG 4000, TRIS-HCL, PH 7.0, 10.0mM 5bDHT, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 186 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→27.84 Å / Num. all: 47344 / Num. obs: 47344 / % possible obs: 97.2 % / Redundancy: 4.7 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 7.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 1 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3 / % possible all: 97.4

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Processing

Software
NameVersionClassification
CNS1.2refinement
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3CMF

3cmf


Resolution: 2→27.84 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2027302.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.257 2035 4.3 %RANDOM
Rwork0.22 ---
obs0.22 47218 96.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.0506 Å2 / ksol: 0.45 e/Å3
Displacement parametersBiso mean: 21.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.35 Å20 Å20 Å2
2---1.37 Å20 Å2
3----0.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2→27.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5254 0 117 588 5959
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_mcbond_it1.251.5
X-RAY DIFFRACTIONc_mcangle_it1.862
X-RAY DIFFRACTIONc_scbond_it1.942
X-RAY DIFFRACTIONc_scangle_it2.692.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.306 343 4.4 %
Rwork0.269 7379 -
obs--97 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3nap.paramnap.top
X-RAY DIFFRACTION4unk.paramunk.top

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