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- PDB-1yb1: Crystal structure of human 17-beta-hydroxysteroid dehydrogenase t... -

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Basic information

Entry
Database: PDB / ID: 1yb1
TitleCrystal structure of human 17-beta-hydroxysteroid dehydrogenase type XI
Components17-beta-hydroxysteroid dehydrogenase type XI
KeywordsOXIDOREDUCTASE / SHORT CHAIN DEHYDROGENASE / HYDROXYSTEROID DEHYDROGENASE / HUMAN / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS Consortium / SGC
Function / homology
Function and homology information


androgen catabolic process / 17-beta-hydroxysteroid dehydrogenase (NAD+) activity / steroid dehydrogenase activity / 17-beta-hydroxysteroid dehydrogenase (NADP+) activity / estrogen biosynthetic process / Estrogen biosynthesis / 17beta-estradiol 17-dehydrogenase / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / lipid droplet / endoplasmic reticulum ...androgen catabolic process / 17-beta-hydroxysteroid dehydrogenase (NAD+) activity / steroid dehydrogenase activity / 17-beta-hydroxysteroid dehydrogenase (NADP+) activity / estrogen biosynthetic process / Estrogen biosynthesis / 17beta-estradiol 17-dehydrogenase / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / lipid droplet / endoplasmic reticulum / cytoplasm / cytosol
Similarity search - Function
short chain dehydrogenase / 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
Androsterone / Estradiol 17-beta-dehydrogenase 11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLukacik, P. / Bunkoczi, G. / Kavanagh, K. / Ng, S. / von Delft, F. / Bray, J. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of human 17-beta-hydroxysteroid dehydrogenase type XI.
Authors: Lukacik, P. / Bunkoczi, G. / Kavanagh, K. / Ng, S. / von Delft, F. / Bray, J. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / Oppermann, U.
History
DepositionDec 18, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jul 3, 2013Group: Non-polymer description
Revision 1.4Jan 31, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 600HETEROGEN AETIOCHOLANOLONE IS ALSO KNOWN AS ANDROSTERONE, 5-ANDROSTAN-3-OL-17-ONE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 17-beta-hydroxysteroid dehydrogenase type XI
B: 17-beta-hydroxysteroid dehydrogenase type XI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,48413
Polymers59,4062
Non-polymers1,07811
Water6,035335
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6390 Å2
ΔGint-136 kcal/mol
Surface area19000 Å2
MethodPISA
2
A: 17-beta-hydroxysteroid dehydrogenase type XI
B: 17-beta-hydroxysteroid dehydrogenase type XI
hetero molecules

A: 17-beta-hydroxysteroid dehydrogenase type XI
B: 17-beta-hydroxysteroid dehydrogenase type XI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,96826
Polymers118,8124
Non-polymers2,15622
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area16600 Å2
ΔGint-280 kcal/mol
Surface area34180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.939, 110.939, 118.013
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 17-beta-hydroxysteroid dehydrogenase type XI


Mass: 29703.123 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHRS8 / Plasmid: P11 (PET11 DERIVATIVE) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3)
References: UniProt: Q8NBQ5, 17beta-estradiol 17-dehydrogenase

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Non-polymers , 5 types, 346 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-AOI / Androsterone / (3alpha,5beta,8alpha,10alpha,13alpha,14beta)-3-hydroxyandrostan-17-one


Mass: 290.440 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H30O2 / Comment: hormone*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 3.1 Å3/Da / Density % sol: 59.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.08M Sodium Citrate pH5, 2.52M Ammonium Sulphate , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Oct 20, 2004
RadiationMonochromator: Multilayer optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→37 Å / Num. all: 61906 / Num. obs: 61906 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.4 % / Rmerge(I) obs: 0.091 / Rsym value: 0.091
Reflection shellResolution: 1.95→2.06 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MR MODEL OBTAINED BY AUTOBUILDING INTO A SELENOMETHIONINE SAD PHASED MAP

Resolution: 1.95→37 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.38 / SU ML: 0.067 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Residual density that is likely due to an alternate main chain conformation of residues 167-170 was not modelled.
RfactorNum. reflection% reflectionSelection details
Rfree0.19212 1763 3.3 %RANDOM
Rwork0.16154 ---
all0.16254 52480 --
obs0.16254 52449 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.395 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2--0.22 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 1.95→37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3651 0 64 335 4050
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223856
X-RAY DIFFRACTIONr_bond_other_d0.0010.023620
X-RAY DIFFRACTIONr_angle_refined_deg1.3441.9685270
X-RAY DIFFRACTIONr_angle_other_deg0.79238416
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0565503
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.69124.37135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.13615641
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2171510
X-RAY DIFFRACTIONr_chiral_restr0.0830.2652
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024188
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02734
X-RAY DIFFRACTIONr_nbd_refined0.2120.2765
X-RAY DIFFRACTIONr_nbd_other0.1580.23473
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21929
X-RAY DIFFRACTIONr_nbtor_other0.0810.22207
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2220
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2010.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.76532603
X-RAY DIFFRACTIONr_mcbond_other0.4231001
X-RAY DIFFRACTIONr_mcangle_it2.62153968
X-RAY DIFFRACTIONr_scbond_it4.20871532
X-RAY DIFFRACTIONr_scangle_it5.858111291
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 141 -
Rwork0.194 3783 -
obs--99.9 %
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)
10.8286-0.08060.04110.94280.19161.22070.01180.15370.1114-0.0979-0.05280.1042-0.0207-0.06870.041-0.10850.0279-0.0054-0.05980.0297-0.04787.4091-19.726311.1586
20.90790.39590.24860.87540.40850.87430.1308-0.046-0.17940.2086-0.0946-0.02760.3428-0.0141-0.03620.07140.01220.0009-0.08530.0022-0.011814.2112-42.963329.3189
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA25 - 26025 - 260
2X-RAY DIFFRACTION2BB25 - 26025 - 260

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