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

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Basic information

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


Estrogen biosynthesis / testosterone 17-beta-dehydrogenase (NADP+) activity / 17beta-estradiol 17-dehydrogenase / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / 2-HYDROXYBENZOIC ACID / 17-beta-hydroxysteroid dehydrogenase 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 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: 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
DepositionOct 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.2Jan 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

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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)29,7855
Polymers28,6831
Non-polymers1,1024
Water55831
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)119,13920
Polymers114,7314
Non-polymers4,40816
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_576x,-y+2,-z+11
Buried area27550 Å2
ΔGint-140 kcal/mol
Surface area32440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.789, 129.789, 129.789
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-304-

PG4

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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 BL21 (bacteria) / 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, 35 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-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID / Salicylic acid


Mass: 138.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O3
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 3.18 Å3/Da / Density % sol: 61.33 %
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: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 2.47→50 Å / Num. obs: 13260 / % possible obs: 100 % / Redundancy: 6.62 % / Rsym value: 0.071 / Net I/σ(I): 19.23
Reflection shellResolution: 2.47→2.62 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 3.49 / Num. unique obs: 2123 / Rsym value: 0.505 / % possible all: 99.9

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Processing

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

5js6


Resolution: 2.47→45.887 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.7
RfactorNum. reflection% reflection
Rfree0.2107 662 4.99 %
Rwork0.1669 --
obs0.1691 13256 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.47→45.887 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1937 0 74 31 2042
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072054
X-RAY DIFFRACTIONf_angle_d0.8952801
X-RAY DIFFRACTIONf_dihedral_angle_d18.881237
X-RAY DIFFRACTIONf_chiral_restr0.053326
X-RAY DIFFRACTIONf_plane_restr0.006385
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4678-2.65830.27521310.20892496X-RAY DIFFRACTION100
2.6583-2.92580.2431310.1922484X-RAY DIFFRACTION100
2.9258-3.34910.28261320.18892505X-RAY DIFFRACTION100
3.3491-4.2190.18211320.1552520X-RAY DIFFRACTION100
4.219-45.89530.18121360.15182589X-RAY DIFFRACTION100
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)
10.0428-0.0457-0.04820.13120.03810.0634-0.0966-0.0096-0.08720.0447-0.1558-0.02340.15980.03-0.19660.42710.01220.39420.1333-0.29190.72221.6537103.566250.7543
20.0107-0.00790.00350.00370.00450.0127-0.0769-0.0191-0.2166-0.01260.02420.00020.10210.1359-0.02610.53260.10070.43610.3235-0.17790.72516.3741103.299440.4185
30.0497-0.04270.07720.1931-0.18040.2559-0.07560.1521-0.1132-0.1166-0.30090.03870.1325-0.1062-0.27690.452-0.10420.23110.2762-0.32690.7574-3.5809109.370440.844
40.2956-0.00320.190.1383-0.11850.4168-0.00080.2873-0.2719-0.1811-0.37680.07720.18450.0839-0.8910.0396-0.08450.12250.1731-0.05940.5129-0.4605122.398948.4128
50.0033-0.00470.01130.03230.01680.0464-0.13840.0841-0.10910.07530.005-0.0020.01910.1473-0.03970.21920.05140.09980.34160.13980.548721.3579118.535655.3899
60.09640.09790.00170.1196-0.09930.4475-0.33210.0105-0.14510.0599-0.17790.00280.28360.0239-0.38240.20930.01930.1571-0.0538-0.01210.71152.4504115.760362.3999
70.00590.0088-0.00670.0011-0.001-0.0034-0.0385-0.08640.1884-0.069-0.0387-0.0081-0.05470.11790.00010.3371-0.00160.03510.40450.09140.568323.72141.791564.296
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 4:39)
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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