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- PDB-3had: BIOCHEMICAL CHARACTERIZATION AND STRUCTURE DETERMINATION OF HUMAN... -

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Basic information

Entry
Database: PDB / ID: 3had
TitleBIOCHEMICAL CHARACTERIZATION AND STRUCTURE DETERMINATION OF HUMAN HEART SHORT CHAIN L-3-HYDROXYACYL COA DEHYDROGENASE PROVIDE INSIGHT INTO CATALYTIC MECHANISM
ComponentsPROTEIN (L-3-HYDROXYACYL COA DEHYDROGENASE)
KeywordsOXIDOREDUCTASE / BETA OXIDATION / SCHAD / CATALYTIC ACTIVITY: L-3-HYDROXYACYL-COA + NAD(+) = 3-OXOACYL-COA + NADH
Function / homology
Function and homology information


Beta oxidation of butanoyl-CoA to acetyl-CoA / Beta oxidation of lauroyl-CoA to decanoyl-CoA-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 / (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity / fatty acid beta-oxidation / NAD+ binding / Mitochondrial protein degradation ...Beta oxidation of butanoyl-CoA to acetyl-CoA / Beta oxidation of lauroyl-CoA to decanoyl-CoA-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 / (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity / fatty acid beta-oxidation / NAD+ binding / Mitochondrial protein degradation / regulation of insulin secretion / response to activity / negative regulation of insulin secretion / response to insulin / positive regulation of cold-induced thermogenesis / transferase activity / spermatogenesis / cell differentiation / mitochondrial matrix / response to xenobiotic stimulus / mitochondrion / nucleoplasm / identical protein binding / cytoplasm
Similarity search - Function
: / 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 ...: / 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 / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsBarycki, J.J. / Bratt, J.M. / Banaszak, L.J.
Citation
Journal: Biochemistry / Year: 1999
Title: Biochemical characterization and crystal structure determination of human heart short chain L-3-hydroxyacyl-CoA dehydrogenase provide insights into catalytic mechanism.
Authors: Barycki, J.J. / O'Brien, L.K. / Bratt, J.M. / Zhang, R. / Sanishvili, R. / Strauss, A.W. / Banaszak, L.J.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1987
Title: Structure of L-3-Hydroxyacyl-Coenzyme A Dehydrogenase: Preliminary Chain Tracing at 2.8-A Resolution
History
DepositionDec 3, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 12, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations / Category: 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 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (L-3-HYDROXYACYL COA DEHYDROGENASE)
B: PROTEIN (L-3-HYDROXYACYL COA DEHYDROGENASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7424
Polymers67,4152
Non-polymers1,3272
Water5,747319
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-44 kcal/mol
Surface area25250 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)50.230, 86.020, 167.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROTEIN (L-3-HYDROXYACYL COA DEHYDROGENASE) / SCHAD


Mass: 33707.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Source: (gene. exp.) Homo sapiens (human)
Description: PROTEIN WAS EXPRESSED WITH A C-TERMINAL HEXAMERIC HISTIDINE TAG.
Organ: HEART / Organelle: MITOCHONDRIAL / Production host: Escherichia coli (E. coli)
References: UniProt: Q16836, 3-hydroxyacyl-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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE TO BE PUBLISHED BY O'BRIEN,SIMS,GIBSON,& STRAUSS

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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: 2.7 Å3/Da / Density % sol: 54.24 %
Crystal growpH: 6.5 / Details: 0.1 M ADA, PH 6.5, 15-20% PEG 4K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
25 mMNAD+1drop
350 mMN-[2-acetamido]-2-iminodiacetic acid1reservoir
414-19 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.03
DetectorType: APS-1 / Detector: CCD / Date: Aug 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 48014 / % possible obs: 94 % / Redundancy: 3.5 % / Biso Wilson estimate: 35.5 Å2 / Rsym value: 0.058 / Net I/σ(I): 7.6
Reflection shellResolution: 2→2.07 Å / % possible all: 83
Reflection
*PLUS
% possible obs: 99.2 % / Rmerge(I) obs: 0.058
Reflection shell
*PLUS
% possible obs: 99.5 %

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS0.3refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2→40 Å / Rfactor Rfree error: 0.006 / Data cutoff high rms absF: 724966.68 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.264 2272 5 %RANDOM
Rwork0.218 ---
obs0.218 45242 92.5 %-
Displacement parametersBiso mean: 47.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4482 0 88 319 4889
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.51.5
X-RAY DIFFRACTIONc_mcangle_it3.92
X-RAY DIFFRACTIONc_scbond_it3.992
X-RAY DIFFRACTIONc_scangle_it5.812.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.374 253 4.7 %
Rwork0.353 5144 -
obs--66.1 %
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78

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