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- PDB-6cge: Crystal structure of human 17beta-HSD type 1 in ternary complex w... -

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Basic information

Entry
Database: PDB / ID: 6cge
TitleCrystal structure of human 17beta-HSD type 1 in ternary complex with PBRM and NADP+
ComponentsEstradiol 17-beta-dehydrogenase 1
KeywordsOXIDOREDUCTASE / Inhibitor / Complex / Hydroxysteroid Dehydrogenase
Function / homology
Function and homology information


estradiol binding / 3(or 17)beta-hydroxysteroid dehydrogenase / 17-beta-hydroxysteroid dehydrogenase (NADP+) activity / estrogen biosynthetic process / testosterone dehydrogenase [NAD(P)] activity / cellular response to metal ion / Estrogen biosynthesis / estradiol 17-beta-dehydrogenase activity / dihydrotestosterone 17-beta-dehydrogenase activity / testosterone dehydrogenase (NAD+) activity ...estradiol binding / 3(or 17)beta-hydroxysteroid dehydrogenase / 17-beta-hydroxysteroid dehydrogenase (NADP+) activity / estrogen biosynthetic process / testosterone dehydrogenase [NAD(P)] activity / cellular response to metal ion / Estrogen biosynthesis / estradiol 17-beta-dehydrogenase activity / dihydrotestosterone 17-beta-dehydrogenase activity / testosterone dehydrogenase (NAD+) activity / testosterone biosynthetic process / testosterone 17-beta-dehydrogenase (NADP+) activity / 17beta-estradiol 17-dehydrogenase / 17-beta-hydroxysteroid dehydrogenase (NAD+) activity / steroid biosynthetic process / NADP+ binding / estrogen metabolic process / The canonical retinoid cycle in rods (twilight vision) / small molecule binding / catalytic activity / steroid binding / bone development / NADP binding / oxidoreductase activity / protein homodimerization activity / cytosol / cytoplasm
Similarity search - Function
17beta-dehydrogenase / short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-F0D / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 17-beta-hydroxysteroid dehydrogenase type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsLi, T. / Lin, S.X.
CitationJournal: J Phys Chem Lett / Year: 2018
Title: Combined Biophysical Chemistry Reveals a New Covalent Inhibitor with a Low-Reactivity Alkyl Halide.
Authors: Li, T. / Maltais, R. / Poirier, D. / Lin, S.X.
History
DepositionFeb 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Estradiol 17-beta-dehydrogenase 1
B: Estradiol 17-beta-dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4586
Polymers69,9782
Non-polymers2,4804
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7060 Å2
ΔGint-33 kcal/mol
Surface area21290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.820, 108.940, 116.360
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Estradiol 17-beta-dehydrogenase 1 / 17-beta-hydroxysteroid dehydrogenase type 1 / 17-beta-HSD 1 / 20 alpha-hydroxysteroid dehydrogenase ...17-beta-hydroxysteroid dehydrogenase type 1 / 17-beta-HSD 1 / 20 alpha-hydroxysteroid dehydrogenase / 20-alpha-HSD / E2DH / Placental 17-beta-hydroxysteroid dehydrogenase / Short chain dehydrogenase/reductase family 28C member 1


Mass: 34989.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSD17B1, E17KSR, EDH17B1, EDH17B2, EDHB17, SDR28C1 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P14061, 17beta-estradiol 17-dehydrogenase
#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-F0D / 3-{[(14beta,16alpha,17alpha)-3-(2-bromoethyl)-17-hydroxyestra-1,3,5(10)-trien-16-yl]methyl}benzamide


Mass: 496.479 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H34BrNO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 1.94 Å3/Da / Density % sol: 36.57 %
Crystal growTemperature: 300 K / Method: evaporation / Details: PEG 8000, potassium phosphate monobasic / PH range: 7.5-7.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 8, 2018
RadiationMonochromator: Kohzu HLD-4 Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.2→24.67 Å / Num. obs: 28372 / % possible obs: 99.5 % / Redundancy: 6.5 % / Rpim(I) all: 0.042 / Rrim(I) all: 0.108 / Rsym value: 0.099 / Net I/av σ(I): 5.5 / Net I/σ(I): 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.2-2.326.10.4771.640060.2080.5210.47798.1
2.32-2.466.20.3762.138260.1630.410.37699.3
2.46-2.636.30.2812.736560.120.3060.28199.9
2.63-2.846.60.1884.134350.0790.2040.188100
2.84-3.116.80.1365.431260.0560.1470.136100
3.11-3.486.90.1085.728670.0440.1170.108100
3.48-4.026.90.101625610.0410.1090.101100
4.02-4.926.80.0738.121690.030.0790.073100
4.92-6.966.70.04212.917440.0180.0460.042100
6.96-24.6666.10.02921.89820.0130.0310.02996.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.589
Highest resolutionLowest resolution
Rotation24.67 Å2.37 Å

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Processing

Software
NameVersionClassification
MOSFLM7.2.0data reduction
SCALA3.3.22data scaling
MOLREP11.4.05phasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JTV
Resolution: 2.2→24.67 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.892 / SU B: 9.442 / SU ML: 0.228 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.344 / ESU R Free: 0.275
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3026 1459 5.2 %RANDOM
Rwork0.2228 ---
obs0.2266 26858 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 113.27 Å2 / Biso mean: 47.099 Å2 / Biso min: 19.09 Å2
Baniso -1Baniso -2Baniso -3
1-1.39 Å2-0 Å2-0 Å2
2---3.48 Å20 Å2
3---2.09 Å2
Refinement stepCycle: final / Resolution: 2.2→24.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4247 0 124 27 4398
Biso mean--58.01 30.49 -
Num. residues----556
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194462
X-RAY DIFFRACTIONr_bond_other_d0.0020.024329
X-RAY DIFFRACTIONr_angle_refined_deg1.6632.026076
X-RAY DIFFRACTIONr_angle_other_deg1.00639918
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5635552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.75122.235179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.0115717
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4851544
X-RAY DIFFRACTIONr_chiral_restr0.0830.2710
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214930
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021014
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 108 -
Rwork0.309 1907 -
all-2015 -
obs--96.23 %

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