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- PDB-3gnc: Crystal structure of Glutaryl-COA dehydrogenase from Burkholderia... -

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Basic information

Entry
Database: PDB / ID: 3gnc
TitleCrystal structure of Glutaryl-COA dehydrogenase from Burkholderia Pseudomallei with fragment 6421
ComponentsGlutaryl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


glutaryl-CoA dehydrogenase (ETF) / glutaryl-CoA dehydrogenase activity / fatty-acyl-CoA biosynthetic process / fatty-acyl-CoA binding / fatty acid beta-oxidation using acyl-CoA dehydrogenase / flavin adenine dinucleotide binding / metal ion binding
Similarity search - Function
: / 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, N-terminal domain ...: / 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, N-terminal domain / Acyl-CoA dehydrogenase, C-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 oxidase/dehydrogenase, middle domain superfamily / 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
Chem-QQQ / glutaryl-CoA dehydrogenase (ETF)
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Probing conformational states of glutaryl-CoA dehydrogenase by fragment screening.
Authors: Begley, D.W. / Davies, D.R. / Hartley, R.C. / Hewitt, S.N. / Rychel, A.L. / Myler, P.J. / Van Voorhis, W.C. / Staker, B.L. / Stewart, L.J.
History
DepositionMar 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Sep 21, 2011Group: Database references
Revision 1.3Sep 6, 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutaryl-CoA dehydrogenase
B: Glutaryl-CoA dehydrogenase
C: Glutaryl-CoA dehydrogenase
D: Glutaryl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,64212
Polymers173,8704
Non-polymers1,7728
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16380 Å2
ΔGint-65 kcal/mol
Surface area51720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.239, 106.104, 144.239
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
Glutaryl-CoA dehydrogenase


Mass: 43467.543 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: BURPS1710b_3237 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3JP94, EC: 1.3.99.7
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-QQQ / 1-(1-methylethyl)-1H-benzimidazole-2-sulfonic acid


Mass: 240.279 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H12N2O3S
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.16 Å3/Da / Density % sol: 43.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 3000, 0.1M HEPES, 0.2M NaCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 81993 / % possible obs: 99.6 % / Redundancy: 7 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 10.8
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.593 / % possible all: 98.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3D6B

3d6b


Resolution: 2.15→46.68 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / SU B: 6.495 / SU ML: 0.168 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.283 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.255 4105 5 %RANDOM
Rwork0.206 ---
obs0.209 81910 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2---0.32 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.15→46.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11546 0 114 210 11870
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02211878
X-RAY DIFFRACTIONr_bond_other_d0.0010.028091
X-RAY DIFFRACTIONr_angle_refined_deg1.2451.97516068
X-RAY DIFFRACTIONr_angle_other_deg0.902319653
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7151501
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.60423.433504
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.756151985
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2511593
X-RAY DIFFRACTIONr_chiral_restr0.0690.21777
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02113231
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022406
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5931.57462
X-RAY DIFFRACTIONr_mcbond_other0.1021.53125
X-RAY DIFFRACTIONr_mcangle_it1.095211862
X-RAY DIFFRACTIONr_scbond_it1.50934416
X-RAY DIFFRACTIONr_scangle_it2.4654.54206
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 291 -
Rwork0.274 5501 -
obs--96.87 %

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