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- PDB-6h0m: 17beta-hydroxysteroid dehydrogenase type 14 mutant K158A in compl... -

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Basic information

Entry
Database: PDB / ID: 6h0m
Title17beta-hydroxysteroid dehydrogenase type 14 mutant K158A in complex with Nicotinamide Adenine Dinucleotide
Components17-beta-hydroxysteroid dehydrogenase 14
KeywordsOXIDOREDUCTASE / mutant hsd cofactor nad complex
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
beta-D-glucopyranose / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 17-beta-hydroxysteroid dehydrogenase 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsBadran, M. / Klebe, G. / Heine, A. / Marchais-Oberwinkler, S.
CitationJournal: To Be Published
Title: 17beta-hydroxysteroid dehydrogenase type 14 mutant K158A in complex with Nicotinamide Adenine Dinucleotide
Authors: Badran, M. / Klebe, G. / Heine, A. / Merabet, A. / Bertoletti, N. / Marchais-Oberwinkler, S.
History
DepositionJul 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)29,2165
Polymers28,2711
Non-polymers9454
Water3,801211
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)116,86420
Polymers113,0854
Non-polymers3,77916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_565x,-y+1,-z1
Buried area23050 Å2
ΔGint-193 kcal/mol
Surface area33130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.590, 91.590, 131.112
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-458-

HOH

21A-541-

HOH

31A-601-

HOH

41A-611-

HOH

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Components

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Protein / Sugars , 2 types, 2 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: 28271.295 Da / Num. of mol.: 1 / Mutation: K158A
Source method: isolated from a genetically manipulated source
Details: mutation K158A / Source: (gene. exp.) Homo sapiens (human) / Gene: HSD17B14, DHRS10, SDR3, SDR47C1, UNQ502/PRO474
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (unknown)
References: UniProt: Q9BPX1, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#5: Sugar ChemComp-BGC / beta-D-glucopyranose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 214 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: 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
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.43 Å3/Da / Density % sol: 49.47 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.1 / Details: PEG 6000 20% W/V HEPES 0.1 M DMSO 5% / PH range: 6.5 - 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 3, 2018
RadiationMonochromator: x-ray / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. obs: 76893 / % possible obs: 99.9 % / Redundancy: 10.1 % / CC1/2: 1 / Rrim(I) all: 0.047 / Rsym value: 0.045 / Χ2: 0.97 / Net I/σ(I): 27.1
Reflection shellResolution: 1.25→1.33 Å / Redundancy: 9.5 % / Mean I/σ(I) obs: 4.1 / Num. unique obs: 12249 / CC1/2: 0.921 / Rrim(I) all: 0.547 / Rsym value: 0.495 / Χ2: 59.77 / % possible all: 99.7

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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: 5ICM
Resolution: 1.25→46.072 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 10.93
RfactorNum. reflection% reflection
Rfree0.1472 3845 5 %
Rwork0.1264 --
obs0.1274 76889 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.25→46.072 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1856 0 61 211 2128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072039
X-RAY DIFFRACTIONf_angle_d1.0152801
X-RAY DIFFRACTIONf_dihedral_angle_d23.305756
X-RAY DIFFRACTIONf_chiral_restr0.078329
X-RAY DIFFRACTIONf_plane_restr0.006390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2495-1.26530.15091400.14932653X-RAY DIFFRACTION99
1.2653-1.2820.17391400.13912663X-RAY DIFFRACTION100
1.282-1.29950.17961400.13292673X-RAY DIFFRACTION100
1.2995-1.31810.16171400.13442647X-RAY DIFFRACTION100
1.3181-1.33780.15551420.12472694X-RAY DIFFRACTION100
1.3378-1.35870.15391410.12652693X-RAY DIFFRACTION100
1.3587-1.38090.14011410.11012667X-RAY DIFFRACTION100
1.3809-1.40480.1381400.10782663X-RAY DIFFRACTION100
1.4048-1.43030.1421410.10762683X-RAY DIFFRACTION100
1.4303-1.45780.13161410.1032684X-RAY DIFFRACTION100
1.4578-1.48760.12731410.10082678X-RAY DIFFRACTION100
1.4876-1.51990.12251410.09462677X-RAY DIFFRACTION100
1.5199-1.55530.11441420.09522696X-RAY DIFFRACTION100
1.5553-1.59420.1151410.09312679X-RAY DIFFRACTION100
1.5942-1.63730.12661430.09812710X-RAY DIFFRACTION100
1.6373-1.68550.12271410.09732682X-RAY DIFFRACTION100
1.6855-1.73990.12311420.10072702X-RAY DIFFRACTION100
1.7399-1.80210.13971420.10262704X-RAY DIFFRACTION100
1.8021-1.87420.1191420.10782692X-RAY DIFFRACTION100
1.8742-1.95950.12861430.11462717X-RAY DIFFRACTION100
1.9595-2.06280.14611420.11882707X-RAY DIFFRACTION100
2.0628-2.19210.12421440.11672728X-RAY DIFFRACTION100
2.1921-2.36130.14871440.12092737X-RAY DIFFRACTION100
2.3613-2.59890.13871440.12462728X-RAY DIFFRACTION100
2.5989-2.97490.12761450.13852769X-RAY DIFFRACTION100
2.9749-3.74780.16861470.14512780X-RAY DIFFRACTION100
3.7478-46.10380.19251550.162938X-RAY DIFFRACTION100

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