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- PDB-6g4l: 17beta-hydroxysteroid Dehydrogenase Type 14 Mutant Y253A in Compl... -

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Basic information

Entry
Database: PDB / ID: 6g4l
Title17beta-hydroxysteroid Dehydrogenase Type 14 Mutant Y253A in Complex With a Non-steroidal Inhibitor
Components17-beta-hydroxysteroid dehydrogenase 14
KeywordsOXIDOREDUCTASE / Inhibitor Complex mutant
Function / homology
Function and homology information


Estrogen biosynthesis / estradiol 17-beta-dehydrogenase [NAD(P)] 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 / Chem-F45 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 17-beta-hydroxysteroid dehydrogenase 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.444 Å
AuthorsBadran, M. / Klebe, G. / Heine, A. / Marchais-Oberwinkler, S.
CitationJournal: J.Steroid Biochem.Mol.Biol. / Year: 2019
Title: Mutational and structural studies uncover crucial amino acids determining activity and stability of 17beta-HSD14
Authors: Badran, M. / Bertoletti, N. / Keils, A. / Heine, A. / Klebe, G. / Marchais-Oberwinkler, S.
History
DepositionMar 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jul 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 / _entity.pdbx_description ..._chem_comp.name / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,5857
Polymers28,2371
Non-polymers1,3486
Water3,945219
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)118,34228
Polymers112,9494
Non-polymers5,39324
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 area23670 Å2
ΔGint-242 kcal/mol
Surface area31150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.423, 91.423, 132.141
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-509-

HOH

21A-579-

HOH

31A-589-

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: 28237.299 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-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9BPX1, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#4: 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 , 5 types, 224 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
#5: Chemical ChemComp-F45 / [6-(3,4-dihydroxyphenyl)pyridin-2-yl](4-fluoro-3-hydroxyphenyl)methanone


Mass: 325.291 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H12FNO4
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.44 Å3/Da / Density % sol: 49.68 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG 6000 50%w/v HEPES 0.1M 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: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.44→50 Å / Num. obs: 50078 / % possible obs: 99.4 % / Redundancy: 8.5 % / CC1/2: 0.999 / Rrim(I) all: 0.059 / Rsym value: 0.055 / Χ2: 0.93 / Net I/σ(I): 20.63
Reflection shellResolution: 1.44→1.53 Å / Redundancy: 8.2 % / Mean I/σ(I) obs: 3.24 / Num. unique obs: 7713 / CC1/2: 0.93 / Rrim(I) all: 0.537 / Rsym value: 0.503 / % possible all: 96.3

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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: 1.444→46.207 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1794 2503 5 %
Rwork0.1564 --
obs0.1576 50051 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.444→46.207 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1828 0 89 219 2136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072046
X-RAY DIFFRACTIONf_angle_d0.9962809
X-RAY DIFFRACTIONf_dihedral_angle_d22.483780
X-RAY DIFFRACTIONf_chiral_restr0.075323
X-RAY DIFFRACTIONf_plane_restr0.006434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4438-1.47160.30541230.26732344X-RAY DIFFRACTION89
1.4716-1.50160.27551370.23792601X-RAY DIFFRACTION100
1.5016-1.53430.21851370.22472612X-RAY DIFFRACTION100
1.5343-1.570.22831380.19532629X-RAY DIFFRACTION100
1.57-1.60920.21111380.18652618X-RAY DIFFRACTION100
1.6092-1.65270.20631390.18342640X-RAY DIFFRACTION100
1.6527-1.70140.19941370.16632607X-RAY DIFFRACTION100
1.7014-1.75630.17751390.16192634X-RAY DIFFRACTION100
1.7563-1.81910.18151390.16172640X-RAY DIFFRACTION100
1.8191-1.89190.20041400.16182650X-RAY DIFFRACTION100
1.8919-1.9780.18861380.15652637X-RAY DIFFRACTION100
1.978-2.08230.19011400.15762646X-RAY DIFFRACTION100
2.0823-2.21280.17981400.14462672X-RAY DIFFRACTION100
2.2128-2.38360.17671400.14032652X-RAY DIFFRACTION100
2.3836-2.62350.1621410.14472677X-RAY DIFFRACTION100
2.6235-3.0030.18381420.15242699X-RAY DIFFRACTION100
3.003-3.78320.17041440.14732730X-RAY DIFFRACTION100
3.7832-46.23060.15151510.14542860X-RAY DIFFRACTION100

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