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- PDB-3eon: 2.55A crystal structure of native glutaryl-coa dehydrogenase from... -

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Basic information

Entry
Database: PDB / ID: 3eon
Title2.55A crystal structure of native glutaryl-coa dehydrogenase from Burkholderia pseudomallei in complex with a small molecule
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
(3,5-difluorophenyl)methanol / glutaryl-CoA dehydrogenase (ETF)
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)173,1695
Polymers173,0254
Non-polymers1441
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15070 Å2
ΔGint-68 kcal/mol
Surface area52580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.409, 106.169, 144.185
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: Chemical ChemComp-341 / (3,5-difluorophenyl)methanol


Mass: 144.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6F2O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.15 Å3/Da / Density % sol: 42.91 %
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: 2.4→50 Å / Num. obs: 59702 / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.118 / Χ2: 1.034 / Net I/σ(I): 16.981
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.4-2.495.90.89458741.027199.8
2.49-2.596.90.75158981.0391100
2.59-2.77.30.59358641.0611100
2.7-2.857.50.46259221.0861100
2.85-3.027.50.31859251.071100
3.02-3.267.50.22159401.0891100
3.26-3.587.50.1359681.0571100
3.58-4.17.40.08259871.0031100
4.1-5.177.30.06260390.9711100
5.17-507.10.03962850.934199.9

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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: 2.55→46.63 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.906 / WRfactor Rfree: 0.257 / WRfactor Rwork: 0.182 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.809 / SU B: 11.431 / SU ML: 0.25 / SU Rfree: 0.347 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.347 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.266 2476 5 %RANDOM
Rwork0.187 ---
all0.191 49412 --
obs0.191 49412 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.89 Å2 / Biso mean: 42.601 Å2 / Biso min: 17.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2---0.14 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.55→46.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11681 0 10 206 11897
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02211911
X-RAY DIFFRACTIONr_angle_refined_deg1.4471.96516082
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.00451505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.33823.391522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.362152037
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6681598
X-RAY DIFFRACTIONr_chiral_restr0.1030.21773
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028980
X-RAY DIFFRACTIONr_nbd_refined0.2220.25757
X-RAY DIFFRACTIONr_nbtor_refined0.310.28066
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2504
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2590.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.210
X-RAY DIFFRACTIONr_mcbond_it0.7471.57699
X-RAY DIFFRACTIONr_mcangle_it1.303211923
X-RAY DIFFRACTIONr_scbond_it1.71434805
X-RAY DIFFRACTIONr_scangle_it2.74.54159
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 179 -
Rwork0.231 3407 -
all-3586 -
obs--99.89 %

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