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- PDB-5jsf: Crystal structure of 17beta-hydroxysteroid dehydrogenase 14 S205 ... -

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Basic information

Entry
Database: PDB / ID: 5jsf
TitleCrystal structure of 17beta-hydroxysteroid dehydrogenase 14 S205 variant in complex with NAD.
Components17-beta-hydroxysteroid dehydrogenase 14
KeywordsOXIDOREDUCTASE / cofactor complex / hydroxysteroid dehydrogenase
Function / homology
Function and homology information


Estrogen biosynthesis / estradiol 17-beta-dehydrogenase activity / testosterone 17-beta-dehydrogenase (NADP+) activity / 17beta-estradiol 17-dehydrogenase / 17-beta-hydroxysteroid dehydrogenase (NAD+) activity / steroid catabolic process / identical protein binding / cytosol
Similarity search - Function
Enoyl-(Acyl carrier protein) reductase / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / TRIETHYLENE GLYCOL / 17-beta-hydroxysteroid dehydrogenase 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.842 Å
AuthorsBertoletti, N. / Marchais-Oberwinkler, S. / Heine, A. / Klebe, G.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationMA-5287/1-1 Germany
German Research FoundationKL-1204/15-1 Germany
CitationJournal: J.Med.Chem. / Year: 2016
Title: New Insights into Human 17 beta-Hydroxysteroid Dehydrogenase Type 14: First Crystal Structures in Complex with a Steroidal Ligand and with a Potent Nonsteroidal Inhibitor.
Authors: Bertoletti, N. / Braun, F. / Lepage, M. / Moller, G. / Adamski, J. / Heine, A. / Klebe, G. / Marchais-Oberwinkler, S.
History
DepositionMay 8, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 17-beta-hydroxysteroid dehydrogenase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5415
Polymers28,6691
Non-polymers8724
Water1,54986
1
A: 17-beta-hydroxysteroid dehydrogenase 14
hetero molecules

A: 17-beta-hydroxysteroid dehydrogenase 14
hetero molecules

A: 17-beta-hydroxysteroid dehydrogenase 14
hetero molecules

A: 17-beta-hydroxysteroid dehydrogenase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,16320
Polymers114,6754
Non-polymers3,48816
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area25200 Å2
ΔGint-264 kcal/mol
Surface area34080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.256, 130.256, 130.256
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-437-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 17-beta-hydroxysteroid dehydrogenase 14 / 17-beta-HSD 14 / 17-beta-hydroxysteroid dehydrogenase DHRS10 / Dehydrogenase/reductase SDR family ...17-beta-HSD 14 / 17-beta-hydroxysteroid dehydrogenase DHRS10 / Dehydrogenase/reductase SDR family member 10 / Retinal short-chain dehydrogenase/reductase retSDR3 / Short chain dehydrogenase/reductase family 47C member 1


Mass: 28668.717 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSD17B14, DHRS10, SDR3, SDR47C1, UNQ502/PRO474 / Production host: Escherichia coli BL21 (unknown) / Variant (production host): pLysS
References: UniProt: Q9BPX1, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor

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Non-polymers , 5 types, 90 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 3.22 Å3/Da / Density % sol: 61.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: HEPES 0.1 M pH 7.00, sodium formate 3.3 M / PH range: 7-8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. obs: 31827 / % possible obs: 99.9 % / Redundancy: 6.66 % / Rsym value: 0.047 / Net I/σ(I): 21.35
Reflection shellResolution: 1.84→1.95 Å / Redundancy: 6.82 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 4.2 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EN4
Resolution: 1.842→46.052 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.56
RfactorNum. reflection% reflection
Rfree0.1866 1592 5 %
Rwork0.1647 --
obs0.1658 31827 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.842→46.052 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1942 0 56 86 2084
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072040
X-RAY DIFFRACTIONf_angle_d0.8172785
X-RAY DIFFRACTIONf_dihedral_angle_d17.7341234
X-RAY DIFFRACTIONf_chiral_restr0.056325
X-RAY DIFFRACTIONf_plane_restr0.005384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8421-1.90160.2661430.2372707X-RAY DIFFRACTION99
1.9016-1.96950.23351440.2072746X-RAY DIFFRACTION100
1.9695-2.04840.25161440.19382722X-RAY DIFFRACTION100
2.0484-2.14160.20141430.18152728X-RAY DIFFRACTION100
2.1416-2.25450.20861430.17342714X-RAY DIFFRACTION100
2.2545-2.39580.2061440.1692734X-RAY DIFFRACTION100
2.3958-2.58070.19851440.16512746X-RAY DIFFRACTION100
2.5807-2.84040.19611450.16542754X-RAY DIFFRACTION100
2.8404-3.25130.17971450.1662751X-RAY DIFFRACTION100
3.2513-4.09590.15821460.15672779X-RAY DIFFRACTION100
4.0959-46.06680.1811510.15472854X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.07860.063-0.23120.0284-0.08821.1981-0.19830.25710.07810.0512-0.14560.32230.1876-0.4874-0.22680.246-0.0019-0.10350.3981-0.17160.7351-26.4623-1.482850.9989
20.5172-0.29170.29610.4679-0.41510.4240.13930.28170.1369-0.1626-0.430.81350.3214-0.7126-0.2330.3614-0.096-0.09220.5359-0.32620.8118-26.6501-6.454440.3665
30.1660.0531-0.10820.4667-0.54740.8302-0.1880.23790.1151-0.2853-0.09730.21870.0579-0.3265-0.29890.35770.0273-0.17250.4058-0.08690.7277-20.62383.522641.0381
40.52010.47050.05880.2838-0.120.377-0.19410.13360.0034-0.1801-0.04870.17720.0357-0.0596-0.05770.26110.0045-0.04470.2403-0.04410.5704-7.40330.438748.5097
50.0237-0.01240.17550.0039-0.0350.3268-0.0144-0.0479-0.0083-0.0481-0.17760.19450.4794-0.0738-0.00510.3626-0.03420.11090.2301-0.07840.608-11.3417-21.377355.541
60.54120.098-0.15860.18080.06440.5333-0.10570.01980.00770.0254-0.16120.20610.0132-0.1603-0.34190.1925-0.0078-0.00450.2773-0.10390.6505-14.125-2.421462.6127
70.0242-0.039-0.0110.03230.0178-0.03230.30060.6099-0.4520.2508-0.2338-0.48770.69170.54270.00110.54150.08370.07480.4379-00.720312.8044-23.963264.5969
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 39 )
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 63 )
3X-RAY DIFFRACTION3chain 'A' and (resid 64 through 93 )
4X-RAY DIFFRACTION4chain 'A' and (resid 94 through 185 )
5X-RAY DIFFRACTION5chain 'A' and (resid 186 through 220 )
6X-RAY DIFFRACTION6chain 'A' and (resid 221 through 254 )
7X-RAY DIFFRACTION7chain 'A' and (resid 255 through 271 )

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