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- PDB-2eba: Crystal structure of the putative glutaryl-CoA dehydrogenase from... -

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Basic information

Entry
Database: PDB / ID: 2eba
TitleCrystal structure of the putative glutaryl-CoA dehydrogenase from thermus thermophilus
ComponentsPutative glutaryl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / glutaryl-CoA dehydrogenase / thermus thermophilius / FAD / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


acyl-CoA dehydrogenase activity / flavin adenine dinucleotide binding
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 / 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 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 / 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 / Putative glutaryl-CoA dehydrogenase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsKumarevel, T.S. / Karthe, P. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of the putative glutaryl-CoA dehydrogenase from thermus thermophilus
Authors: Kumarevel, T.S. / Karthe, P. / Kuramitsu, S. / Yokoyama, S.
History
DepositionFeb 7, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 1, 2007Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 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_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: Putative glutaryl-CoA dehydrogenase
C: Putative glutaryl-CoA dehydrogenase
D: Putative glutaryl-CoA dehydrogenase
E: Putative glutaryl-CoA dehydrogenase
F: Putative glutaryl-CoA dehydrogenase
G: Putative glutaryl-CoA dehydrogenase
H: Putative glutaryl-CoA dehydrogenase
I: Putative glutaryl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)348,95816
Polymers342,6748
Non-polymers6,2848
Water10,809600
1
A: Putative glutaryl-CoA dehydrogenase
C: Putative glutaryl-CoA dehydrogenase
D: Putative glutaryl-CoA dehydrogenase
E: Putative glutaryl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,4798
Polymers171,3374
Non-polymers3,1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22760 Å2
ΔGint-109 kcal/mol
Surface area44110 Å2
MethodPISA, PQS
2
F: Putative glutaryl-CoA dehydrogenase
G: Putative glutaryl-CoA dehydrogenase
H: Putative glutaryl-CoA dehydrogenase
I: Putative glutaryl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,4798
Polymers171,3374
Non-polymers3,1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22820 Å2
ΔGint-107 kcal/mol
Surface area43830 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)75.239, 86.239, 157.418
Angle α, β, γ (deg.)75.92, 81.25, 64.24
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Putative glutaryl-CoA dehydrogenase


Mass: 42834.195 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA0789 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q5SK63, glutaryl-CoA dehydrogenase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 600 / 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: 2.6 Å3/Da / Density % sol: 52.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.6M Mg Formate, 0.1M Sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 2, 2004
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. all: 131981 / Num. obs: 131981 / % possible obs: 77 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.4 % / Biso Wilson estimate: 7.6 Å2 / Rmerge(I) obs: 0.128
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.393 / Num. unique all: 11253 / % possible all: 66.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
CCP4(MOLREP)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SIR

1sir


Resolution: 2.21→19.96 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 42790.03 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.275 850 0.7 %RANDOM
Rwork0.26 ---
obs0.26 125477 72.8 %-
all-131981 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.0323 Å2 / ksol: 0.41722 e/Å3
Displacement parametersBiso mean: 21.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.61 Å2-2.78 Å2-3.89 Å2
2--2.45 Å21.53 Å2
3---0.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.21→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23888 0 424 600 24912
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.017
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_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d4.05
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.961.5
X-RAY DIFFRACTIONc_mcangle_it1.512
X-RAY DIFFRACTIONc_scbond_it1.592
X-RAY DIFFRACTIONc_scangle_it2.32.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.292 105 0.7 %
Rwork0.322 14882 -
obs--51.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3dna-rna_rep.paramdna-rna_rep.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5fad-new.paramfad-new.top

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