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- PDB-4l1w: Crystal Structuer of Human 3-alpha Hydroxysteroid Dehydrogenase T... -

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Basic information

Entry
Database: PDB / ID: 4l1w
TitleCrystal Structuer of Human 3-alpha Hydroxysteroid Dehydrogenase Type 3 in Complex with NADP+ and Progesterone
ComponentsAldo-keto reductase family 1 member C2
KeywordsOXIDOREDUCTASE / ALPHA-BETA BARREL / HUMAN 3-ALPHA HSD3 / AKR / AKR1C2 / ALDO-KETO REDUCTASE / NADPH
Function / homology
Function and homology information


indanol dehydrogenase / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase / 3(or 17)alpha-hydroxysteroid dehydrogenase / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity / indanol dehydrogenase activity / cellular response to prostaglandin D stimulus / 3alpha-hydroxysteroid 3-dehydrogenase / phenanthrene 9,10-monooxygenase activity / cellular response to jasmonic acid stimulus / 3alpha(or 20beta)-hydroxysteroid dehydrogenase ...indanol dehydrogenase / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase / 3(or 17)alpha-hydroxysteroid dehydrogenase / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity / indanol dehydrogenase activity / cellular response to prostaglandin D stimulus / 3alpha-hydroxysteroid 3-dehydrogenase / phenanthrene 9,10-monooxygenase activity / cellular response to jasmonic acid stimulus / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase activity / androsterone dehydrogenase activity / ketosteroid monooxygenase activity / steroid dehydrogenase activity / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / progesterone metabolic process / 17beta-estradiol 17-dehydrogenase / carboxylic acid binding / 17-beta-hydroxysteroid dehydrogenase (NAD+) activity / Oxidoreductases / daunorubicin metabolic process / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / doxorubicin metabolic process / bile acid binding / prostaglandin metabolic process / alditol:NADP+ 1-oxidoreductase activity / steroid metabolic process / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / epithelial cell differentiation / digestion / positive regulation of protein kinase B signaling / G protein-coupled receptor signaling pathway / positive regulation of cell population proliferation / cytosol
Similarity search - Function
Aldo-keto reductase family 1 member C / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / NADP-dependent oxidoreductase domain / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel ...Aldo-keto reductase family 1 member C / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / NADP-dependent oxidoreductase domain / 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 / PROGESTERONE / Aldo-keto reductase family 1 member C2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZhang, B. / Hu, X.-J. / Lin, S.-X.
CitationJournal: J.Steroid Biochem.Mol.Biol. / Year: 2014
Title: Human 3-alpha hydroxysteroid dehydrogenase type 3 (3 alpha-HSD3): The V54L mutation restricting the steroid alternative binding and enhancing the 20 alpha-HSD activity
Authors: Zhang, B. / Zhu, D.-W. / Hu, X.-J. / Zhou, M. / Shang, P. / Lin, S.-X.
History
DepositionJun 3, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aldo-keto reductase family 1 member C2
B: Aldo-keto reductase family 1 member C2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2218
Polymers73,9132
Non-polymers2,3086
Water6,648369
1
A: Aldo-keto reductase family 1 member C2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1104
Polymers36,9561
Non-polymers1,1543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Aldo-keto reductase family 1 member C2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1104
Polymers36,9561
Non-polymers1,1543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.800, 86.820, 76.490
Angle α, β, γ (deg.)90.00, 105.96, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A-1 - 323
2010B-1 - 323

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Components

#1: Protein Aldo-keto reductase family 1 member C2 / 3-alpha-HSD3 / Chlordecone reductase homolog HAKRD / Dihydrodiol dehydrogenase 2 / DD-2 / DD2 / ...3-alpha-HSD3 / Chlordecone reductase homolog HAKRD / Dihydrodiol dehydrogenase 2 / DD-2 / DD2 / Dihydrodiol dehydrogenase/bile acid-binding protein / DD/BABP / Trans-1 / 2-dihydrobenzene-1 / 2-diol dehydrogenase / Type III 3-alpha-hydroxysteroid dehydrogenase


Mass: 36956.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1C2 / Production host: Escherichia coli (E. coli)
References: UniProt: P52895, trans-1,2-dihydrobenzene-1,2-diol dehydrogenase, EC: 1.1.1.213
#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-STR / PROGESTERONE / Progesterone


Mass: 314.462 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30O2 / Comment: hormone*YM
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 2.28 Å3/Da / Density % sol: 46.06 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 25% PEG3350, 0.1M Sodium Cacodylate, 0.2M Ammonium Sulfate, 0.8mM Progesterone, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 31, 2012
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.2→21.5 Å / Num. obs: 32561 / % possible obs: 96.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.037
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.056 / Num. unique all: 4701 / % possible all: 95.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J96
Resolution: 2.2→21.35 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.921 / SU B: 4.264 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.282 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19351 1640 5 %RANDOM
Rwork0.14573 ---
obs0.14816 30919 96.41 %-
all-32561 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.739 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å2-0 Å2-0.98 Å2
2---0.35 Å2-0 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.2→21.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5204 0 152 369 5725
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0195521
X-RAY DIFFRACTIONr_bond_other_d0.0060.025276
X-RAY DIFFRACTIONr_angle_refined_deg1.9022.0067520
X-RAY DIFFRACTIONr_angle_other_deg1.205312180
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8325654
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.47624.325252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.12315944
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5061531
X-RAY DIFFRACTIONr_chiral_restr0.1070.2826
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0216121
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021248
Refine LS restraints NCS

Ens-ID: 1 / Number: 21131 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.207 125 -
Rwork0.155 2213 -
obs--95.78 %

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