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- PDB-3hdh: PIG HEART SHORT CHAIN L-3-HYDROXYACYL COA DEHYDROGENASE REVISITED... -

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Basic information

Entry
Database: PDB / ID: 3hdh
TitlePIG HEART SHORT CHAIN L-3-HYDROXYACYL COA DEHYDROGENASE REVISITED: SEQUENCE ANALYSIS AND CRYSTAL STRUCTURE DETERMINATION
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 lauroyl-CoA to decanoyl-CoA-CoA / Beta oxidation of hexanoyl-CoA to butanoyl-CoA / Beta oxidation of butanoyl-CoA to acetyl-CoA / Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA / Beta oxidation of octanoyl-CoA to hexanoyl-CoA / 3-hydroxyacyl-CoA dehydrogenase / (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity / Mitochondrial protein degradation / fatty acid beta-oxidation / NAD+ binding ...Beta oxidation of lauroyl-CoA to decanoyl-CoA-CoA / Beta oxidation of hexanoyl-CoA to butanoyl-CoA / Beta oxidation of butanoyl-CoA to acetyl-CoA / Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA / Beta oxidation of octanoyl-CoA to hexanoyl-CoA / 3-hydroxyacyl-CoA dehydrogenase / (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity / Mitochondrial protein degradation / fatty acid beta-oxidation / NAD+ binding / regulation of insulin secretion / positive regulation of cold-induced thermogenesis / spermatogenesis / cell differentiation / mitochondrial matrix / mitochondrion / nucleoplasm / identical protein binding
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 speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBarycki, J.J. / O'Brien, L.K. / Birktoft, J.J. / Strauss, A.W. / Banaszak, L.J.
Citation
Journal: Protein Sci. / Year: 1999
Title: Pig heart short chain L-3-hydroxyacyl-CoA dehydrogenase revisited: sequence analysis and crystal structure determination.
Authors: Barycki, J.J. / O'Brien, L.K. / Birktoft, J.J. / 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
Authors: Birktoft, J.J. / Holden, H.M. / Hamlin, R. / Xuong, N.H. / Banaszak, L.J.
History
DepositionApr 13, 1999Deposition site: BNL / Processing site: NDB
Revision 1.0Oct 8, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: PROTEIN (L-3-HYDROXYACYL COA DEHYDROGENASE)
B: PROTEIN (L-3-HYDROXYACYL COA DEHYDROGENASE)
C: PROTEIN (L-3-HYDROXYACYL COA DEHYDROGENASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,4856
Polymers98,4953
Non-polymers1,9903
Water41423
1
A: PROTEIN (L-3-HYDROXYACYL COA DEHYDROGENASE)
B: PROTEIN (L-3-HYDROXYACYL COA DEHYDROGENASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9904
Polymers65,6632
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-40 kcal/mol
Surface area25160 Å2
MethodPISA
2
C: PROTEIN (L-3-HYDROXYACYL COA DEHYDROGENASE)
hetero molecules

C: PROTEIN (L-3-HYDROXYACYL COA DEHYDROGENASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9904
Polymers65,6632
Non-polymers1,3272
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)227.200, 82.100, 124.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsUNUSUAL SITUATION OF 3 SUBUNITS CONTAINED WITHIN THE ASYMMETRIC UNIT FOR A DIMERIC ENZYME.

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Components

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


Mass: 32831.719 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: HEART / Organelle: MITOCHONDRIAL
References: UniProt: P00348, 3-hydroxyacyl-CoA dehydrogenase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


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


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58 % / Description: USED DIMER AS A PROBE.
Crystal growpH: 8 / Details: 10 MM TRIS, PH 8.0, + 1MM DTT + 11-14% PEG 6K
Crystal grow
*PLUS
Method: gel filtration
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mMTris1drop
21 mMdithiothreitol1drop
30.05 %1dropNaN3
45 mg/mlprotein1drop
511-14 %(w/v)PEG60001reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceWavelength: 1.54
DetectorDate: Jan 1, 1985
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 28840 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 58.7 Å2 / Rsym value: 0.046 / Net I/σ(I): 4.9
Reflection shellResolution: 2.8→2.97 Å / % possible all: 85
Reflection
*PLUS
% possible obs: 98 % / Rmerge(I) obs: 0.046

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Processing

Software
NameClassification
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HAD

3had


Resolution: 2.8→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high rms absF: 6104754.86 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
Details: BULK SOLVENT MODEL USED POOR ELECTRON DENSITY OBSERVED FOR THIRD SUBUNIT (SUBUNIT C). THREE BREAKS WERE OBSERVED IN THE DENSITY AND SEVERAL RESIDUES HAVE BEEN ASSIGNED OCCUPANCIES OF 0.5
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1201 4.9 %RANDOM
Rwork0.223 ---
obs-24618 84.7 %-
Displacement parametersBiso mean: 62.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6507 0 132 23 6662
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.11.5
X-RAY DIFFRACTIONc_mcangle_it5.072
X-RAY DIFFRACTIONc_scbond_it4.772
X-RAY DIFFRACTIONc_scangle_it7.142.5
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.329 160 5.3 %
Rwork0.306 2850 -
obs--63.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2NAD.PARWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMNAD.TOP
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refinement
*PLUS
σ(F): 1 / % reflection Rfree: 4.9 % / Rfactor obs: 0.223
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 62.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.329 / % reflection Rfree: 5.3 % / Rfactor Rwork: 0.306

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