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- PDB-2o23: The structure of wild-type human HADH2 (17beta-hydroxysteroid deh... -

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Basic information

Entry
Database: PDB / ID: 2o23
TitleThe structure of wild-type human HADH2 (17beta-hydroxysteroid dehydrogenase type 10) bound to NAD+ at 1.2 A
ComponentsHADH2 protein
KeywordsOXIDOREDUCTASE / HSD17B10 / SCHAD / ERAB / Type II HADH / 2-Methyl-3-hydroxybutyryl-CoA dehydrogenase / MHBD / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


brexanolone metabolic process / isoursodeoxycholate 7-beta-dehydrogenase (NAD+) activity / ursodeoxycholate 7-beta-dehydrogenase (NAD+) activity / 3-hydroxy-2-methylbutyryl-CoA dehydrogenase / 3-hydroxy-2-methylbutyryl-CoA dehydrogenase activity / mitochondrial tRNA methylation / rRNA processing in the mitochondrion / tRNA processing in the mitochondrion / mitochondrial ribonuclease P complex / mitochondrial tRNA 5'-end processing ...brexanolone metabolic process / isoursodeoxycholate 7-beta-dehydrogenase (NAD+) activity / ursodeoxycholate 7-beta-dehydrogenase (NAD+) activity / 3-hydroxy-2-methylbutyryl-CoA dehydrogenase / 3-hydroxy-2-methylbutyryl-CoA dehydrogenase activity / mitochondrial tRNA methylation / rRNA processing in the mitochondrion / tRNA processing in the mitochondrion / mitochondrial ribonuclease P complex / mitochondrial tRNA 5'-end processing / chenodeoxycholate 7-alpha-dehydrogenase (NAD+) activity / mitochondrial tRNA 3'-end processing / tRNA modification in the mitochondrion / 17-beta-hydroxysteroid dehydrogenase (NAD+) activity / 7alpha-hydroxysteroid dehydrogenase / cholate 7-alpha-dehydrogenase activity / C21-steroid hormone metabolic process / testosterone dehydrogenase [NAD(P)+] activity / tRNA methyltransferase complex / 3-hydroxyacyl-CoA dehydrogenase / isoleucine catabolic process / 3alpha(17beta)-hydroxysteroid dehydrogenase (NAD+) / 3-hydroxyacyl-CoA dehydrogenase activity / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase activity / bile acid biosynthetic process / testosterone dehydrogenase (NAD+) activity / Branched-chain amino acid catabolism / 17beta-estradiol 17-dehydrogenase / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / estrogen metabolic process / fatty acid beta-oxidation / mitochondrial nucleoid / androgen metabolic process / Mitochondrial protein degradation / mitochondrion organization / fatty acid metabolic process / lipid metabolic process / protein homotetramerization / tRNA binding / mitochondrial matrix / mitochondrion / RNA binding / plasma membrane / cytoplasm
Similarity search - Function
short chain dehydrogenase / 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 / 3-hydroxyacyl-CoA dehydrogenase type-2 / 3-hydroxyacyl-CoA dehydrogenase type-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsKavanagh, K.L. / Shafqat, N. / Scholer, K. / Debreczeni, J. / Zschocke, J. / von Delft, F. / Weigelt, J. / Arrowsmith, C. / Sundstrom, M. / Edwards, A. ...Kavanagh, K.L. / Shafqat, N. / Scholer, K. / Debreczeni, J. / Zschocke, J. / von Delft, F. / Weigelt, J. / Arrowsmith, C. / Sundstrom, M. / Edwards, A. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The structure of wild-type human HADH2 (17beta-hydroxysteroid dehydrogenase type 10) bound to NAD+ at 1.2 A
Authors: KAVANAGH, K.L. / SHAFQAT, N. / SCHOLER, K. / DEBRECZENI, J. / ZSCHOCKE, J. / von Delft, F. / WEIGELT, J. / ARROWSMITH, C. / SUNDSTROM, M. / EDWARDS, A. / OPPERMANN, U.
History
DepositionNov 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jan 31, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.5Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HADH2 protein
B: HADH2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9925
Polymers54,5732
Non-polymers1,4193
Water11,061614
1
A: HADH2 protein
B: HADH2 protein
hetero molecules

A: HADH2 protein
B: HADH2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,98310
Polymers109,1454
Non-polymers2,8386
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area20000 Å2
ΔGint-121 kcal/mol
Surface area30710 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)117.037, 117.037, 69.087
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-843-

HOH

21A-866-

HOH

31A-882-

HOH

41A-903-

HOH

51A-1068-

HOH

61B-880-

HOH

71B-980-

HOH

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Components

#1: Protein HADH2 protein / Hydroxyacyl-Coenzyme A dehydrogenase / type II


Mass: 27286.348 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HADH2 / Plasmid: pET11-derivative / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q6IBS9, UniProt: Q99714*PLUS, 3-hydroxy-2-methylbutyryl-CoA dehydrogenase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 614 / 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: 2.5 Å3/Da / Density % sol: 50.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 25.5% PEG 3350, 15% glycerol, 0.17 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9687
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 1, 2006
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9687 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. all: 168585 / Num. obs: 168585 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 11 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 8.1
Reflection shellResolution: 1.2→1.26 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 24386 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345data collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1U7T

1u7t


Resolution: 1.2→50 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.028 / SU ML: 0.02 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.028 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15395 1996 1.2 %RANDOM
Rwork0.12264 ---
all0.123 166548 --
obs0.123 166548 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.171 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å2-0.22 Å20 Å2
2---0.45 Å20 Å2
3---0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3582 0 94 614 4290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223917
X-RAY DIFFRACTIONr_bond_other_d0.0010.022567
X-RAY DIFFRACTIONr_angle_refined_deg1.552.0075372
X-RAY DIFFRACTIONr_angle_other_deg0.96136330
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8575552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.88824.653144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.22215612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1411525
X-RAY DIFFRACTIONr_chiral_restr0.0910.2639
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024480
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02723
X-RAY DIFFRACTIONr_nbd_refined0.2240.2736
X-RAY DIFFRACTIONr_nbd_other0.1940.22733
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21932
X-RAY DIFFRACTIONr_nbtor_other0.0860.21900
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2401
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2570.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2150.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.254
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.5132784
X-RAY DIFFRACTIONr_mcbond_other2.79631084
X-RAY DIFFRACTIONr_mcangle_it5.14954119
X-RAY DIFFRACTIONr_scbond_it7.41671428
X-RAY DIFFRACTIONr_scangle_it8.854111231
X-RAY DIFFRACTIONr_rigid_bond_restr3.73737038
X-RAY DIFFRACTIONr_sphericity_free20.1493621
X-RAY DIFFRACTIONr_sphericity_bonded7.41336404
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 157 -
Rwork0.238 12109 -
obs--98.25 %

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