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- PDB-1siq: The Crystal Structure and Mechanism of Human Glutaryl-CoA Dehydro... -

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Basic information

Entry
Database: PDB / ID: 1siq
TitleThe Crystal Structure and Mechanism of Human Glutaryl-CoA Dehydrogenase
ComponentsGlutaryl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / Acyl-CoA Dehydrogenase / Decarboxylation / Flavin Protein
Function / homology
Function and homology information


glutaryl-CoA dehydrogenase (ETF) / glutaryl-CoA dehydrogenase activity / fatty-acyl-CoA biosynthetic process / tryptophan metabolic process / fatty acid beta-oxidation using acyl-CoA dehydrogenase / Lysine catabolism / fatty-acyl-CoA binding / flavin adenine dinucleotide binding / mitochondrial matrix / mitochondrion
Similarity search - Function
Acyl-CoA dehydrogenases signature 1. / Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal ...Acyl-CoA dehydrogenases signature 1. / Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Up-down Bundle / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Glutaryl-CoA dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWang, M. / Fu, Z. / Paschke, R. / Goodman, S. / Frerman, F.E. / Kim, J.J.
CitationJournal: Biochemistry / Year: 2004
Title: Crystal Structures of Human Glutaryl-CoA Dehydrogenase with and without an Alternate Substrate: Structural Bases of Dehydrogenation and Decarboxylation Reactions
Authors: Fu, Z. / Wang, M. / Paschke, R. / Rao, K.S. / Frerman, F.E. / Kim, J.J.
History
DepositionMar 1, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Glutaryl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0482
Polymers43,2621
Non-polymers7861
Water2,306128
1
A: Glutaryl-CoA dehydrogenase
hetero molecules

A: Glutaryl-CoA dehydrogenase
hetero molecules

A: Glutaryl-CoA dehydrogenase
hetero molecules

A: Glutaryl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,1928
Polymers173,0504
Non-polymers3,1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
crystal symmetry operation9_554-x,-x+y,-z-1/31
crystal symmetry operation12_564x,x-y+1,-z-1/31
Buried area25040 Å2
ΔGint-124 kcal/mol
Surface area45920 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)116.960, 116.960, 128.020
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Glutaryl-CoA dehydrogenase / / GCD


Mass: 43262.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Strain: bacterial strain:BL21 / References: UniProt: Q92947, glutaryl-CoA dehydrogenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.95 Å3/Da / Density % sol: 57.93 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MES buffer. PEG5KMME, Ammonium Sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 30, 2000 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→29.86 Å / Num. all: 28832 / Num. obs: 28832 / % possible obs: 93.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Biso Wilson estimate: 9 Å2 / Rsym value: 0.067 / Net I/σ(I): 9.4
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 2087 / Rsym value: 0.25 / % possible all: 69.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→29.86 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 126683.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1998 6.9 %RANDOM
Rwork0.198 ---
obs0.198 28832 93.8 %-
all-28832 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.9802 Å2 / ksol: 0.336348 e/Å3
Displacement parametersBiso mean: 27.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.55 Å20.94 Å20 Å2
2--1.55 Å20 Å2
3----3.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.1→29.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3011 0 53 128 3192
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d21.1
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it2.581.5
X-RAY DIFFRACTIONc_mcangle_it3.952
X-RAY DIFFRACTIONc_scbond_it4.412
X-RAY DIFFRACTIONc_scangle_it6.442.5
LS refinement shellResolution: 2.1→2.18 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.361 151 7.2 %
Rwork0.351 1936 -
obs--69.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4FAD.PARAMFAD.TOP

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