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- PDB-6gtu: 17beta-hydroxysteroid dehydrogenase 14 variant T205 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 6gtu
Title17beta-hydroxysteroid dehydrogenase 14 variant T205 in complex with fragment J6
Components17-beta-hydroxysteroid dehydrogenase 14
KeywordsOXIDOREDUCTASE / fragments / soaking / 17b-HSD14
Function / homology
Function and homology information


D-threo-aldose 1-dehydrogenase / D-threo-aldose 1-dehydrogenase activity / Estrogen biosynthesis / L-fucose catabolic process / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / steroid catabolic process / identical protein binding / cytosol
Similarity search - Function
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / 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
N-(1,3-benzodioxol-5-ylmethyl)cyclopentanamine / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / TRIETHYLENE GLYCOL / L-fucose dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsBertoletti, N. / Heine, A. / Marchais-Oberwinkler, S. / Klebe, G.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationMA-5287/1-1 Germany
German Research FoundationKL-1204/15-1 Germany
CitationJournal: To Be Published
Title: X-ray Crystallographic Fragment screening and Hit Optimization
Authors: Bertoletti, N. / Braun, F. / Zara, L. / Metz, A. / Heine, A. / Marchais-Oberwinkler, S. / Klebe, G.
History
DepositionJun 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)29,7515
Polymers28,6831
Non-polymers1,0684
Water1,38777
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)119,00420
Polymers114,7314
Non-polymers4,27316
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 area26020 Å2
ΔGint-207 kcal/mol
Surface area32250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.510, 129.510, 129.510
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-416-

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: 28682.740 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 (E. coli) / Strain (production host): BL21(DE3) / 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, 81 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-45N / N-(1,3-benzodioxol-5-ylmethyl)cyclopentanamine


Mass: 219.280 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H17NO2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


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


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


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.16 Å3/Da / Density % sol: 61.08 % / Description: 3D crystal, cubic shape
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: HEPES 0.1 M pH 7.00, sodium formate 3.3 M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 17085 / % possible obs: 98.5 % / Redundancy: 11.3 % / Rsym value: 0.07 / Net I/σ(I): 24.4
Reflection shellResolution: 2.25→2.39 Å / Redundancy: 11.2 % / Mean I/σ(I) obs: 4.7 / Num. unique obs: 2783 / Rsym value: 0.5 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JS6

5js6


Resolution: 2.25→45.789 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.73
RfactorNum. reflection% reflection
Rfree0.1916 855 5 %
Rwork0.1577 --
obs0.1595 17084 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.25→45.789 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1942 0 71 77 2090
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072064
X-RAY DIFFRACTIONf_angle_d0.82819
X-RAY DIFFRACTIONf_dihedral_angle_d16.591254
X-RAY DIFFRACTIONf_chiral_restr0.051327
X-RAY DIFFRACTIONf_plane_restr0.005397
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2497-2.39070.25231430.18912712X-RAY DIFFRACTION99
2.3907-2.57520.18661430.16472713X-RAY DIFFRACTION100
2.5752-2.83430.19771430.14972722X-RAY DIFFRACTION100
2.8343-3.24440.19581440.15952732X-RAY DIFFRACTION100
3.2444-4.08720.20751410.15032682X-RAY DIFFRACTION98
4.0872-45.79820.1681410.15772668X-RAY DIFFRACTION94
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0172-0.00390.0360.0284-0.01730.0998-0.0558-0.07440.1648-0.0724-0.0757-0.0294-0.2536-0.0987-0.08240.3549-0.0051-0.11550.2280.11390.5966-1.585926.077850.4114
20.02330.0004-0.02210.0025-0.0070.0271-0.22190.0020.28030.03610.0588-0.0317-0.2705-0.1618-0.0050.53460.0633-0.25690.38330.12680.7039-6.237226.954840.4942
30.06780.0071-0.1070.2620.16230.30380.00030.09630.1577-0.0951-0.2132-0.1046-0.09910.0662-0.21210.3484-0.0229-0.07960.31140.21740.61373.519920.504640.7777
40.0809-0.0913-0.15280.18370.20680.513-0.12170.19990.1972-0.1549-0.13230.0053-0.1045-0.0504-0.11630.2365-0.0208-0.04970.23620.0640.51150.40847.352848.2127
50.0013-0.00310.01230.0207-0.01010.121-0.1430.08240.20740.10370.036-0.00180.003-0.1714-0.00440.2260.0323-0.09010.3026-0.07520.5028-21.27911.270855.2062
60.07790.1011-0.00310.32710.02970.2702-0.23330.04550.17-0.0227-0.1248-0.0338-0.1818-0.0485-0.53780.2135-0.0372-0.1418-0.1579-0.01150.6666-2.4314.032262.2632
70.0147-0.00190.01010.001-0.0012-0.002-0.067-0.1819-0.1256-0.12120.0387-0.01020.0495-0.14230.00020.2839-0.018-0.08630.3637-0.08840.5826-23.7889-12.741364.2568
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 5:39)
2X-RAY DIFFRACTION2(chain A and resid 40:63)
3X-RAY DIFFRACTION3(chain A and resid 64:93)
4X-RAY DIFFRACTION4(chain A and resid 94:185)
5X-RAY DIFFRACTION5(chain A and resid 186:220)
6X-RAY DIFFRACTION6(chain A and resid 221:254)
7X-RAY DIFFRACTION7(chain A and resid 255:271)

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