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- PDB-2pd6: Structure of human hydroxysteroid dehydrogenase type 8, HSD17B8 -

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Basic information

Entry
Database: PDB / ID: 2pd6
TitleStructure of human hydroxysteroid dehydrogenase type 8, HSD17B8
ComponentsEstradiol 17-beta-dehydrogenase 8
KeywordsOXIDOREDUCTASE / short-chain dehydrogenase/reductase / steroid metabolism / lipid metabolism / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


(3R)-hydroxyacyl-CoA dehydrogenase (NAD) activity / : / estrogen biosynthetic process / 3alpha(17beta)-hydroxysteroid dehydrogenase (NAD+) / estradiol 17-beta-dehydrogenase [NAD(P)] activity / Fatty acyl-CoA biosynthesis / testosterone dehydrogenase (NAD+) activity / NADH binding / oxidoreductase complex / 17beta-estradiol 17-dehydrogenase ...(3R)-hydroxyacyl-CoA dehydrogenase (NAD) activity / : / estrogen biosynthetic process / 3alpha(17beta)-hydroxysteroid dehydrogenase (NAD+) / estradiol 17-beta-dehydrogenase [NAD(P)] activity / Fatty acyl-CoA biosynthesis / testosterone dehydrogenase (NAD+) activity / NADH binding / oxidoreductase complex / 17beta-estradiol 17-dehydrogenase / 17-beta-hydroxysteroid dehydrogenase (NAD+) activity / mitochondrial envelope / protein heterotetramerization / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / androgen metabolic process / quinone binding / fatty acid biosynthetic process / mitochondrial matrix / plasma membrane
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / (3R)-3-hydroxyacyl-CoA dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTurnbull, A.P. / Salah, E. / Gileadi, O. / Savitsky, P. / Guo, K. / Bunkoczi, G. / Pike, A.C.W. / Ugochukwu, E. / Umeano, C. / von Delft, F. ...Turnbull, A.P. / Salah, E. / Gileadi, O. / Savitsky, P. / Guo, K. / Bunkoczi, G. / Pike, A.C.W. / Ugochukwu, E. / Umeano, C. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Sundstrom, M. / Edwards, A. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Structure of human hydroxysteroid dehydrogenase type 8, HSD17B8
Authors: Turnbull, A.P. / Salah, E. / Gileadi, O. / Savitsky, P. / Guo, K. / Bunkoczi, G. / Pike, A.C.W. / Ugochukwu, E. / Umeano, C. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Sundstrom, M. ...Authors: Turnbull, A.P. / Salah, E. / Gileadi, O. / Savitsky, P. / Guo, K. / Bunkoczi, G. / Pike, A.C.W. / Ugochukwu, E. / Umeano, C. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Sundstrom, M. / Edwards, A. / Oppermann, U. / Structural Genomics Consortium (SGC)
History
DepositionMar 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Estradiol 17-beta-dehydrogenase 8
B: Estradiol 17-beta-dehydrogenase 8
C: Estradiol 17-beta-dehydrogenase 8
D: Estradiol 17-beta-dehydrogenase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,5198
Polymers109,8654
Non-polymers2,6544
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16020 Å2
ΔGint-107 kcal/mol
Surface area30920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.839, 62.429, 102.439
Angle α, β, γ (deg.)90.00, 99.22, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Estradiol 17-beta-dehydrogenase 8 / 17-beta-HSD 8 / 17- beta-hydroxysteroid dehydrogenase 8 / Protein Ke6 / Ke-6


Mass: 27466.223 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSD17B8, FABGL, HKE6, RING2 / Plasmid: pNIC-CTHF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-pRARE2
References: UniProt: Q92506, 17beta-estradiol 17-dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 1.98 Å3/Da / Density % sol: 37.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 200 mM sodium fluoride, 20% PEG3350, 10% ethylene glycol plus 5mM NAD+, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00234 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 22, 2007
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00234 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 54998 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.117
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.759 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Swissmodel based on pdb entries 1Q7B and 1EDO
Resolution: 2→46 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 8.266 / SU ML: 0.116 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.191 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22667 2937 5.1 %RANDOM
Rwork0.18394 ---
all0.18616 54998 --
obs0.18616 54998 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.061 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å20 Å2-0.05 Å2
2--0.86 Å20 Å2
3---0.22 Å2
Refinement stepCycle: LAST / Resolution: 2→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6605 0 176 207 6988
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226884
X-RAY DIFFRACTIONr_bond_other_d0.0010.024212
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.9919415
X-RAY DIFFRACTIONr_angle_other_deg0.8963.00310285
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6415952
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.9624.932219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.58415981
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4211531
X-RAY DIFFRACTIONr_chiral_restr0.0750.21178
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027813
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021238
X-RAY DIFFRACTIONr_nbd_refined0.2030.21446
X-RAY DIFFRACTIONr_nbd_other0.1830.24385
X-RAY DIFFRACTIONr_nbtor_refined0.1680.23515
X-RAY DIFFRACTIONr_nbtor_other0.0870.23431
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2248
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2730.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4330.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8021.54850
X-RAY DIFFRACTIONr_mcbond_other0.1941.51976
X-RAY DIFFRACTIONr_mcangle_it1.22827436
X-RAY DIFFRACTIONr_scbond_it2.02532326
X-RAY DIFFRACTIONr_scangle_it3.0624.51975
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 201 -
Rwork0.211 3823 -
obs--95.24 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.93490.1689-0.6681.7596-0.06651.3582-0.0158-0.03480.04430.08310.0630.04630.0210.0421-0.0473-0.08640.0351-0.0209-0.1885-0.0341-0.14423.538815.750947.1102
22.4002-0.79540.21243.3671-1.53434.42430.02230.23450.2025-0.2-0.05020.0991-0.2272-0.03090.0279-0.082-0.00080-0.1956-0.0288-0.1248-1.440510.79635.1852
32.79950.3003-0.76671.45710.41252.0321-0.08090.1713-0.22830.0012-0.01170.06460.2515-0.29660.0927-0.0304-0.0223-0.0202-0.0706-0.0668-0.1041-6.7717-7.549418.0771
42.6791-0.91161.1632.2695-0.94133.2920.04080.1768-0.25840.0399-0.05-0.02510.29190.08640.0092-0.04360.00860.0019-0.1433-0.0534-0.0709-0.5244-2.655529.6385
52.53710.2765-0.29881.30920.07811.1354-0.11140.4003-0.193-0.23110.1718-0.20480.07390.1117-0.0604-0.01650.01440.01460.0335-0.1014-0.090419.0059-0.82633.7849
62.7229-1.24950.36234.113-0.8071.9319-0.06550.27080.0744-0.06810.10010.0367-0.0870.1267-0.0346-0.08940.0121-0.0089-0.0011-0.0189-0.128520.338411.325811.4314
71.93930.0875-0.7790.7576-0.21782.08460.0347-0.09110.07630.04640.0874-0.2389-0.04110.5451-0.1221-0.1151-0.0065-0.0370.075-0.1006-0.01531.887918.889934.3952
82.5232-0.89170.05914.7952-0.64082.71730.018-0.1234-0.19480.29590.1182-0.13230.32230.4825-0.1362-0.07840.0581-0.04940.027-0.0565-0.07228.26258.715526.3915
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 551 - 51
2X-RAY DIFFRACTION1AA68 - 18764 - 183
3X-RAY DIFFRACTION2AA188 - 259184 - 255
4X-RAY DIFFRACTION3BB9 - 555 - 51
5X-RAY DIFFRACTION3BB67 - 18363 - 179
6X-RAY DIFFRACTION4BB184 - 260180 - 256
7X-RAY DIFFRACTION5CC12 - 558 - 51
8X-RAY DIFFRACTION5CC68 - 18764 - 183
9X-RAY DIFFRACTION6CC188 - 260184 - 256
10X-RAY DIFFRACTION7DD7 - 553 - 51
11X-RAY DIFFRACTION7DD68 - 18364 - 179
12X-RAY DIFFRACTION8DD184 - 260180 - 256

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