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- PDB-3bv7: Crystal structure of Delta(4)-3-ketosteroid 5-beta-reductase in c... -

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Basic information

Entry
Database: PDB / ID: 3bv7
TitleCrystal structure of Delta(4)-3-ketosteroid 5-beta-reductase in complex with NADP and glycerol. Resolution: 1.79 A.
Components3-oxo-5-beta-steroid 4-dehydrogenase
KeywordsOXIDOREDUCTASE / 5-beta-reductase / glycerol / AKR1A1 / Bile acid catabolism / Disease mutation / Lipid metabolism / NADP / Steroid metabolism
Function / homology
Function and homology information


Delta4-3-oxosteroid 5beta-reductase / steroid dehydrogenase activity / bile acid catabolic process / C21-steroid hormone metabolic process / Delta4-3-oxosteroid 5beta-reductase activity / ketosteroid monooxygenase activity / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / bile acid biosynthetic process / : / cholesterol catabolic process ...Delta4-3-oxosteroid 5beta-reductase / steroid dehydrogenase activity / bile acid catabolic process / C21-steroid hormone metabolic process / Delta4-3-oxosteroid 5beta-reductase activity / ketosteroid monooxygenase activity / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / bile acid biosynthetic process / : / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aldo-keto reductase family 1 member D1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.79 Å
AuthorsDi Costanzo, L. / Drury, J. / Penning, T.M. / Christianson, D.W.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Crystal Structure of Human Liver {Delta}4-3-Ketosteroid 5{beta}-Reductase (AKR1D1) and Implications for Substrate Binding and Catalysis.
Authors: Di Costanzo, L. / Drury, J.E. / Penning, T.M. / Christianson, D.W.
History
DepositionJan 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Aug 30, 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_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)76,6197
Polymers74,8562
Non-polymers1,7635
Water6,269348
1
A: 3-oxo-5-beta-steroid 4-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4485
Polymers37,4281
Non-polymers1,0204
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)38,1712
Polymers37,4281
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.826, 109.833, 129.186
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: 37427.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1D1, SRD5B1 / Organ: liver / Plasmid: pET28a-AKR1D1 / Production host: Escherichia coli (E. coli)
References: UniProt: P51857, Delta4-3-oxosteroid 5beta-reductase
#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.36 Å3/Da / Density % sol: 47.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein: 5.0 mg/mL AKR1D1, 2.0 mM NADPH, 2.0 mM 5-beta-cholestan-3-one, 10.0 mM Tris (pH 7.4). Precipitant buffer: 0.1 M Tris (pH 7.0), 10-20% (wt/vol) PEG 4000, 10% isopropanol., pH 7.5, ...Details: Protein: 5.0 mg/mL AKR1D1, 2.0 mM NADPH, 2.0 mM 5-beta-cholestan-3-one, 10.0 mM Tris (pH 7.4). Precipitant buffer: 0.1 M Tris (pH 7.0), 10-20% (wt/vol) PEG 4000, 10% isopropanol., pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 23, 2007
Details: Rosenbaum-Rock monochromator high-resolution double-crystal Si (111) sagittal focusing. Rosenbaum-Rock vertical focusing mirror.
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. all: 66774 / Num. obs: 66774 / % possible obs: 98.6 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 20.5
Reflection shellResolution: 1.79→1.85 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.4 / Num. unique all: 6684 / % possible all: 100

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Processing

Software
NameVersionClassification
SHELXL-97refinement
CNSrefinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3BUR

3bur


Resolution: 1.79→50 Å
RfactorNum. reflectionSelection details
Rfree0.2571 2800 RANDOM
all0.2361 63320 -
obs0.2361 63320 -
Refinement stepCycle: LAST / Resolution: 1.79→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5254 0 114 348 5716
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.012
X-RAY DIFFRACTIONs_bond_d0.02
X-RAY DIFFRACTIONs_from_restr_planes0.024
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.031
X-RAY DIFFRACTIONs_approx_iso_adps0

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