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- PDB-3eom: 2.4 A crystal structure of native glutaryl-coa dehydrogenase from... -

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Basic information

Entry
Database: PDB / ID: 3eom
Title2.4 A crystal structure of native glutaryl-coa dehydrogenase from Burkholderia pseudomallei
ComponentsGlutaryl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / BURKHOLDERIA / PSEUDOMALLEI / GLUTARYL-COA / DEHYDROGENASE / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / SSGCID
Function / homology
Function and homology information


glutaryl-CoA dehydrogenase activity / glutaryl-CoA dehydrogenase (ETF) / 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
glutaryl-CoA dehydrogenase (ETF)
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.398 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
DepositionSep 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 21, 2011Group: Database references
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)173,0254
Polymers173,0254
Non-polymers00
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14710 Å2
ΔGint-68 kcal/mol
Surface area52930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.115, 106.768, 145.425
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Glutaryl-CoA dehydrogenase / E.C.1.3.99.7


Mass: 43256.328 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710B / Gene: BURPS1710B_2458, BURPS1710b_3237, MSRB / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3JP94, EC: 1.3.99.7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.2 Å3/Da / Density % sol: 44.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7.5
Details: 20% PEG 3000, 0.1M HEPES pH 7.5, 0.2M NaCl, VAPOR DIFFUSION, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 1, 2008 / Details: ADJUSTABLE FOCUSING MIRRORS
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.398→50 Å / Num. obs: 60203 / % possible obs: 99.5 % / Redundancy: 7 % / Rmerge(I) obs: 0.084 / Χ2: 1.127 / Net I/σ(I): 23.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.398-2.496.50.65858320.79198.2
2.49-2.5970.50859290.84198.9
2.59-2.770.3859340.867199.5
2.7-2.857.10.28459690.979199.7
2.85-3.027.20.19159921.14199.9
3.02-3.267.30.13560201.321199.9
3.26-3.587.30.09160061.5361100
3.58-4.17.30.07360961.414199.9
4.1-5.177.10.06761201.3341100
5.17-506.70.05763050.954199.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.87 Å37.95 Å
Translation2.87 Å37.95 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.398→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.263 / WRfactor Rwork: 0.205 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.786 / SU B: 10.108 / SU ML: 0.234 / SU R Cruickshank DPI: 0.57 / SU Rfree: 0.294 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.58 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.264 3035 5.1 %RANDOM
Rwork0.211 ---
all0.213 60090 --
obs0.213 60090 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.37 Å2 / Biso mean: 60.415 Å2 / Biso min: 34.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2--0.13 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 2.398→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11741 0 0 167 11908
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02211971
X-RAY DIFFRACTIONr_angle_refined_deg1.2621.96316167
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.63951515
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.96223.39528
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.271152050
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1411599
X-RAY DIFFRACTIONr_chiral_restr0.0880.21783
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029040
X-RAY DIFFRACTIONr_nbd_refined0.2050.25693
X-RAY DIFFRACTIONr_nbtor_refined0.2990.28131
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2471
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2320.26
X-RAY DIFFRACTIONr_mcbond_it0.6221.57756
X-RAY DIFFRACTIONr_mcangle_it1.092211990
X-RAY DIFFRACTIONr_scbond_it1.30934811
X-RAY DIFFRACTIONr_scangle_it2.0744.54177
LS refinement shellResolution: 2.398→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 212 -
Rwork0.284 4003 -
all-4215 -
obs--95.71 %

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