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

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Basic information

Entry
Database: PDB / ID: 3cas
TitleCrystal structure of 5beta-reductase (AKR1D1) in complex with NADP+ and 4-androstenedione
Components3-oxo-5-beta-steroid 4-dehydrogenase
KeywordsOXIDOREDUCTASE / 5b-reductase / 5beta-reductase / 5b-red / AKR1D1 / AKR / aldo-keto reductase / NADP / androstenedione / NADPH / substrate inhibition / Bile acid catabolism / Cytoplasm / Disease mutation / Lipid metabolism / 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
4-ANDROSTENE-3-17-DIONE / BETA-MERCAPTOETHANOL / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aldo-keto reductase family 1 member D1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsFaucher, F. / Cantin, L. / Breton, R.
CitationJournal: Biochemistry / Year: 2008
Title: Crystal Structures of Human Delta4-3-Ketosteroid 5beta-Reductase (AKR1D1) Reveal the Presence of an Alternative Binding Site Responsible for Substrate Inhibition (dagger) (,) (double dagger).
Authors: Faucher, F. / Cantin, L. / Luu-The, V. / Labrie, F. / Breton, R.
History
DepositionFeb 20, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)77,36613
Polymers74,8562
Non-polymers2,51011
Water8,305461
1
A: 3-oxo-5-beta-steroid 4-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7227
Polymers37,4281
Non-polymers1,2946
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)38,6446
Polymers37,4281
Non-polymers1,2165
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.410, 110.870, 130.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 37427.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1D1, SRD5B1 / Plasmid: pGEX6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLys
References: UniProt: P51857, Delta4-3-oxosteroid 5beta-reductase

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Non-polymers , 5 types, 472 molecules

#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-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ASD / 4-ANDROSTENE-3-17-DIONE / Androstenedione


Mass: 286.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H26O2 / Comment: hormone*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 461 / 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: 2.43 Å3/Da / Density % sol: 49.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.7
Details: PEG-4000 21%, 0.1M Tris, MPD 5% CaCl2 0.05M, pH 7.7, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 11, 2007 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→19.63 Å / Num. all: 50230 / Num. obs: 48139 / % possible obs: 95.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 8 % / Biso Wilson estimate: 18.989 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.124 / Net I/σ(I): 21.26
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 5.1 / Num. measured obs: 21901 / Num. unique all: 6750 / Num. unique obs: 5727 / Rsym value: 0.278 / % possible all: 84.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
CNS1.1refinement
PDB_EXTRACT3.004data extraction
CrystalCleardata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.63 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2672150 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2435 5.1 %RANDOM
Rwork0.208 ---
all-48139 --
obs-48139 95.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.874 Å2 / ksol: 0.335 e/Å3
Displacement parametersBiso mean: 14 Å2
Baniso -1Baniso -2Baniso -3
1-1.4 Å20 Å20 Å2
2--0.26 Å20 Å2
3----1.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2→19.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5296 0 166 461 5923
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_mcbond_it1.131.5
X-RAY DIFFRACTIONc_mcangle_it1.642
X-RAY DIFFRACTIONc_scbond_it1.772
X-RAY DIFFRACTIONc_scangle_it2.492.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.302 341 4.9 %
Rwork0.268 6671 -
all-7012 -
obs--85.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ligands_.paramligands_.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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