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- PDB-3rqs: Crystal Structure of human L-3- Hydroxyacyl-CoA dehydrogenase (EC... -

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Basic information

Entry
Database: PDB / ID: 3rqs
TitleCrystal Structure of human L-3- Hydroxyacyl-CoA dehydrogenase (EC1.1.1.35) from mitochondria at the resolution 2.0 A, Northeast Structural Genomics Consortium Target HR487, Mitochondrial Protein Partnership
ComponentsHydroxyacyl-coenzyme A dehydrogenase, mitochondrial
KeywordsOXIDOREDUCTASE / Structural Genomics / PSI-biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Mitochondrial Protein Partnership / MPP
Function / homology
Function and homology information


Beta oxidation of lauroyl-CoA to decanoyl-CoA-CoA / Beta oxidation of butanoyl-CoA to acetyl-CoA / Beta oxidation of hexanoyl-CoA to butanoyl-CoA / Beta oxidation of octanoyl-CoA to hexanoyl-CoA / Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA / 3-hydroxyacyl-CoA dehydrogenase / 3-hydroxyacyl-CoA dehydrogenase activity / fatty acid beta-oxidation / regulation of insulin secretion / NAD+ binding ...Beta oxidation of lauroyl-CoA to decanoyl-CoA-CoA / Beta oxidation of butanoyl-CoA to acetyl-CoA / Beta oxidation of hexanoyl-CoA to butanoyl-CoA / Beta oxidation of octanoyl-CoA to hexanoyl-CoA / Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA / 3-hydroxyacyl-CoA dehydrogenase / 3-hydroxyacyl-CoA dehydrogenase activity / fatty acid beta-oxidation / regulation of insulin secretion / NAD+ binding / negative regulation of insulin secretion / Mitochondrial protein degradation / response to activity / response to insulin / positive regulation of cold-induced thermogenesis / transferase activity / mitochondrial matrix / response to xenobiotic stimulus / mitochondrion / nucleoplasm / identical protein binding / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1150 / 3-hydroxyacyl-CoA dehydrogenase / 3-hydroxyacyl-CoA dehydrogenase, conserved site / 3-hydroxyacyl-CoA dehydrogenase signature. / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1150 / 3-hydroxyacyl-CoA dehydrogenase / 3-hydroxyacyl-CoA dehydrogenase, conserved site / 3-hydroxyacyl-CoA dehydrogenase signature. / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å
AuthorsKuzin, A. / Su, M. / Seetharaman, J. / Patel, P. / Xiao, R. / Ciccosanti, C. / Shastry, R. / Everett, J.K. / Nair, R. / Acton, T.B. ...Kuzin, A. / Su, M. / Seetharaman, J. / Patel, P. / Xiao, R. / Ciccosanti, C. / Shastry, R. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) / Mitochondrial Protein Partnership (MPP)
CitationJournal: To be published
Title: Northeast Structural Genomics Consortium Target HR487
Authors: Kuzin, A. / Su, M. / Seetharaman, J. / Patel, P. / Xiao, R. / Ciccosanti, C. / Shastry, R. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionApr 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Structure summary
Revision 1.3Aug 3, 2011Group: Structure summary
Revision 1.4Sep 13, 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 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial
B: Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7189
Polymers72,0742
Non-polymers6457
Water9,422523
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-34 kcal/mol
Surface area27030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.691, 85.761, 165.614
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial / HCDH / Medium and short-chain L-3-hydroxyacyl-coenzyme A dehydrogenase / Short-chain 3-hydroxyacyl- ...HCDH / Medium and short-chain L-3-hydroxyacyl-coenzyme A dehydrogenase / Short-chain 3-hydroxyacyl-CoA dehydrogenase


Mass: 36036.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HADH, HAD, HADHSC, SCHAD / Production host: Escherichia coli (E. coli)
References: UniProt: Q16836, 3-hydroxyacyl-CoA dehydrogenase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 523 / 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: 2.45 Å3/Da / Density % sol: 49.76 %
Crystal growTemperature: 277 K / Method: macrobatch under oil / pH: 4.2
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution: 0.1M Potassium phosphate dibasic (K2HPO4), 0.1M Sodium Citrate, 20% (w/v) PEG 4000, macrobatch ...Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution: 0.1M Potassium phosphate dibasic (K2HPO4), 0.1M Sodium Citrate, 20% (w/v) PEG 4000, macrobatch under oil, temperature 277KK

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 23, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 48661 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 25.61 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 21.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.94 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIX1.7_646refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F0Y

1f0y


Resolution: 2.001→29.824 Å / Occupancy max: 1 / Occupancy min: 0.46 / FOM work R set: 0.882 / SU ML: 0.23 / σ(F): 1.35 / Phase error: 18.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.204 2459 5.05 %random
Rwork0.166 ---
obs0.168 48661 99.92 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.875 Å2 / ksol: 0.363 e/Å3
Displacement parametersBiso max: 200.42 Å2 / Biso mean: 30.092 Å2 / Biso min: 8.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.726 Å2-0 Å20 Å2
2---1.774 Å2-0 Å2
3---2.5 Å2
Refinement stepCycle: LAST / Resolution: 2.001→29.824 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4677 0 42 523 5242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074849
X-RAY DIFFRACTIONf_angle_d0.986544
X-RAY DIFFRACTIONf_chiral_restr0.064757
X-RAY DIFFRACTIONf_plane_restr0.004827
X-RAY DIFFRACTIONf_dihedral_angle_d13.0031816
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.001-2.0390.251570.2012461261899
2.039-2.0810.2711160.18425822698100
2.081-2.1260.2231330.17925082641100
2.126-2.1750.2071360.16625322668100
2.175-2.230.2091370.16225382675100
2.23-2.290.2151330.15325132646100
2.29-2.3570.21440.15825682712100
2.357-2.4330.231250.16725322657100
2.433-2.520.2211340.17925562690100
2.52-2.6210.2451240.17425832707100
2.621-2.740.2121450.17225362681100
2.74-2.8850.221360.17225352671100
2.885-3.0650.2011340.17425932727100
3.065-3.3020.2111350.16825842719100
3.302-3.6340.1621380.15525702708100
3.634-4.1580.1821520.15226012753100
4.158-5.2340.1661330.14426472780100
5.234-29.8270.2341470.1842763291099
Refinement TLS params.Method: refined / Origin x: 21.9098 Å / Origin y: 66.1095 Å / Origin z: 106.1312 Å
111213212223313233
T0.0812 Å2-0.0064 Å20.0167 Å2-0.1023 Å2-0.0035 Å2--0.092 Å2
L0.0066 °20.0645 °2-0.0111 °2-0.0852 °2-0.0272 °2--0.2093 °2
S-0.0081 Å °0.0411 Å °-0.0295 Å °-0.0146 Å °0.0067 Å °0.0339 Å °-0.0177 Å °-0.0197 Å °0.0008 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA23 - 314
2X-RAY DIFFRACTION1allB-1 - 314
3X-RAY DIFFRACTION1allB - A1 - 318
4X-RAY DIFFRACTION1all1 - 525

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