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- PDB-5ics: Crystal structure of 17beta-hydroxysteroid dehydrogenase type 14 ... -

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Basic information

Entry
Database: PDB / ID: 5ics
TitleCrystal structure of 17beta-hydroxysteroid dehydrogenase type 14 apoenzyme.
Components17-beta-hydroxysteroid dehydrogenase 14
KeywordsOXIDOREDUCTASE / apoenzyme / hydroxysteroid dehydrogenase
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
L-fucose dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 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
DepositionFeb 23, 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
Revision 1.3Jan 10, 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 1.4Nov 13, 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
C: 17-beta-hydroxysteroid dehydrogenase 14
D: 17-beta-hydroxysteroid dehydrogenase 14
F: 17-beta-hydroxysteroid dehydrogenase 14


Theoretical massNumber of molelcules
Total (without water)114,6754
Polymers114,6754
Non-polymers00
Water13,241735
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15800 Å2
ΔGint-126 kcal/mol
Surface area35030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.039, 92.191, 87.280
Angle α, β, γ (deg.)90.00, 114.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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.: 4
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 735 / Source method: isolated from a natural source / Formula: H2O
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: 2.5 Å3/Da / Density % sol: 49.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: Sodium acetate 0.1 M; PEG 400 30%; ammonium acetate 0.2 M.
PH range: 4.6-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9148 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9148 Å / Relative weight: 1
ReflectionResolution: 1.52→50 Å / Num. obs: 169468 / % possible obs: 99.5 % / Redundancy: 3.8 % / Rsym value: 0.058 / Net I/σ(I): 15.23
Reflection shellResolution: 1.52→1.61 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.74 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1-2155_1492: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EN4

5en4


Resolution: 1.52→43.949 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.85
RfactorNum. reflection% reflection
Rfree0.1642 8474 5 %
Rwork0.1291 --
obs0.1308 169454 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.52→43.949 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7475 0 0 735 8210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087767
X-RAY DIFFRACTIONf_angle_d0.93710589
X-RAY DIFFRACTIONf_dihedral_angle_d17.1374697
X-RAY DIFFRACTIONf_chiral_restr0.061238
X-RAY DIFFRACTIONf_plane_restr0.0071396
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5188-1.53610.2092700.17675122X-RAY DIFFRACTION95
1.5361-1.55420.21342800.16855322X-RAY DIFFRACTION100
1.5542-1.57310.22322830.1625386X-RAY DIFFRACTION100
1.5731-1.5930.2262810.15535327X-RAY DIFFRACTION100
1.593-1.6140.21962830.15975390X-RAY DIFFRACTION100
1.614-1.63610.20752820.15045342X-RAY DIFFRACTION100
1.6361-1.65950.20452790.14965317X-RAY DIFFRACTION100
1.6595-1.68430.19042850.14055397X-RAY DIFFRACTION100
1.6843-1.71060.16812840.13425397X-RAY DIFFRACTION100
1.7106-1.73860.17232800.12685321X-RAY DIFFRACTION100
1.7386-1.76860.18572810.12255344X-RAY DIFFRACTION100
1.7686-1.80080.1672830.11765376X-RAY DIFFRACTION100
1.8008-1.83540.15432830.11265372X-RAY DIFFRACTION100
1.8354-1.87290.1632830.11295386X-RAY DIFFRACTION100
1.8729-1.91360.14882810.11385341X-RAY DIFFRACTION100
1.9136-1.95810.15912820.11485349X-RAY DIFFRACTION100
1.9581-2.00710.15952820.1135369X-RAY DIFFRACTION100
2.0071-2.06130.16342830.11375365X-RAY DIFFRACTION100
2.0613-2.1220.14742820.11295366X-RAY DIFFRACTION100
2.122-2.19050.15142840.10815389X-RAY DIFFRACTION100
2.1905-2.26880.15552830.11065382X-RAY DIFFRACTION100
2.2688-2.35960.15232820.11285367X-RAY DIFFRACTION100
2.3596-2.4670.15942830.11145368X-RAY DIFFRACTION100
2.467-2.5970.15372840.11655389X-RAY DIFFRACTION100
2.597-2.75970.16172830.1265388X-RAY DIFFRACTION100
2.7597-2.97270.15392840.13385399X-RAY DIFFRACTION100
2.9727-3.27180.1712840.13265397X-RAY DIFFRACTION100
3.2718-3.7450.15662840.13855396X-RAY DIFFRACTION100
3.745-4.71750.14812860.12855432X-RAY DIFFRACTION100
4.7175-43.96740.16832900.15795484X-RAY DIFFRACTION99

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