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

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Basic information

Entry
Database: PDB / ID: 6cgc
TitleCrystal structure of human 17beta-HSD type 1 in ternary complex with 2-MeO-CC-156 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 / dihydrotestosterone 17-beta-dehydrogenase activity / testosterone dehydrogenase (NAD+) activity / testosterone biosynthetic process ...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 / dihydrotestosterone 17-beta-dehydrogenase activity / testosterone dehydrogenase (NAD+) activity / testosterone biosynthetic process / testosterone 17-beta-dehydrogenase (NADP+) activity / 17beta-estradiol 17-dehydrogenase / estradiol 17-beta-dehydrogenase [NAD(P)] activity / steroid biosynthetic process / estrogen metabolic process / NADP+ binding / lysosome organization / The canonical retinoid cycle in rods (twilight vision) / small molecule binding / adipose tissue development / catalytic activity / skeletal muscle tissue development / steroid binding / bone development / gene expression / NADP binding / 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-F0A / 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: 2.1 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 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)72,3366
Polymers69,9782
Non-polymers2,3584
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6820 Å2
ΔGint-35 kcal/mol
Surface area21460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.750, 107.980, 115.720
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-F0A / 3-{[(9beta,14beta,16alpha,17alpha)-3,17-dihydroxy-2-methoxyestra-1,3,5(10)-trien-16-yl]methyl}benzamide


Mass: 435.555 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 1.86 Å3/Da / Density % sol: 34 %
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: 2.1→24.661 Å / Num. obs: 28809 / % possible obs: 91.9 % / Redundancy: 6 % / Rpim(I) all: 0.055 / Rrim(I) all: 0.144 / Rsym value: 0.132 / Net I/av σ(I): 3.7 / Net I/σ(I): 7.4 / Num. measured all: 173088
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.1-2.2160.4191.839290.1780.4560.41987.7
2.21-2.3560.3352.136990.1430.3660.33587.2
2.35-2.515.90.2732.735090.1160.2980.27387.3
2.51-2.715.80.2163.332970.0930.2360.21688.6
2.71-2.975.70.1664.131580.0710.1810.16690.8
2.97-3.325.60.1414.530290.0610.1540.14196.5
3.32-3.836.10.1354.527990.0580.1480.13599.9
3.83-4.76.70.1274.624170.0510.1370.127100
4.7-6.646.70.0865.818890.0350.0930.086100
6.64-24.6616.20.04611.910830.020.050.04696.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.563
Highest resolutionLowest resolution
Rotation24.66 Å2.26 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

1jtv


Resolution: 2.1→24.66 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.911 / SU B: 7.593 / SU ML: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.302 / ESU R Free: 0.23
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2595 1481 5.2 %RANDOM
Rwork0.2028 ---
obs0.2057 27231 91.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 127.08 Å2 / Biso mean: 38.889 Å2 / Biso min: 18.43 Å2
Baniso -1Baniso -2Baniso -3
1-1.83 Å20 Å20 Å2
2---3.84 Å20 Å2
3---2.01 Å2
Refinement stepCycle: final / Resolution: 2.1→24.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4244 0 122 33 4399
Biso mean--50.37 27.48 -
Num. residues----555
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194462
X-RAY DIFFRACTIONr_bond_other_d0.0020.024324
X-RAY DIFFRACTIONr_angle_refined_deg1.7932.0176080
X-RAY DIFFRACTIONr_angle_other_deg1.03139909
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5785553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.43122.265181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.11815717
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6691544
X-RAY DIFFRACTIONr_chiral_restr0.090.2709
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214944
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021018
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 93 -
Rwork0.267 1875 -
all-1968 -
obs--87.27 %

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