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

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Basic information

Entry
Database: PDB / ID: 3bur
TitleCrystal structure of Delta(4)-3-ketosteroid 5-beta-reductase in complex with NADP and TESTOSTERONE. RESOLUTION: 1.62 A.
Components3-oxo-5-beta-steroid 4-dehydrogenase
KeywordsOXIDOREDUCTASE / 5BETA-REDUCTASE / CATALYTIC TETRAD / TESTOSTERONE / NADP / Bile acid catabolism / Disease mutation / Lipid metabolism / Steroid metabolism
Function / homology
Function and homology information


Delta4-3-oxosteroid 5beta-reductase / C21-steroid hormone metabolic process / bile acid catabolic process / steroid dehydrogenase activity / Delta4-3-oxosteroid 5beta-reductase activity / ketosteroid monooxygenase activity / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / aldo-keto reductase (NADPH) activity / bile acid biosynthetic process / aldose reductase (NADPH) activity ...Delta4-3-oxosteroid 5beta-reductase / C21-steroid hormone metabolic process / bile acid catabolic process / steroid dehydrogenase activity / Delta4-3-oxosteroid 5beta-reductase activity / ketosteroid monooxygenase activity / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / aldo-keto reductase (NADPH) activity / bile acid biosynthetic process / aldose reductase (NADPH) activity / androgen metabolic process / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / cholesterol catabolic process / 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 / TESTOSTERONE / Aldo-keto reductase family 1 member D1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsDi Costanzo, L. / 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 3, 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 1.2Aug 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)77,84016
Polymers74,8562
Non-polymers2,98514
Water8,971498
1
A: 3-oxo-5-beta-steroid 4-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0129
Polymers37,4281
Non-polymers1,5848
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)38,8287
Polymers37,4281
Non-polymers1,4006
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.819, 109.985, 128.915
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 / Fragment: AKRD1 / Mutation: Aldo-keto reductase family 1 member D1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: Liver / 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-TES / TESTOSTERONE


Mass: 288.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H28O2 / Comment: hormone*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 498 / 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: 47.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10-20% WT/VOL PEG 4000; 1O% ISOPROPANOL; 100 MM TRIS PH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 8, 2007 / Details: KOHZU: Double Crystal Si(111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.62→50 Å / Num. all: 86037 / Num. obs: 86037 / % possible obs: 96 % / Redundancy: 4.5 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 20.3
Reflection shellResolution: 1.62→1.68 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.7 / Num. unique all: 7952 / % possible all: 90

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
SHELXL-97refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J96

1j96


Resolution: 1.62→50 Å / Isotropic thermal model: ISOTROPIC / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.248 4306 RANDOM
Rwork0.228 --
all0.228 81663 -
obs-81663 -
Refinement stepCycle: LAST / Resolution: 1.62→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5254 0 198 498 5950
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.023
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.044
X-RAY DIFFRACTIONs_from_restr_planes0.025
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.016

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