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- PDB-3swo: Crystal structure of a glutaryl-coa dehydrogenase from mycobacter... -

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Basic information

Entry
Database: PDB / ID: 3swo
TitleCrystal structure of a glutaryl-coa dehydrogenase from mycobacterium smegmatis in complex with FADH2
ComponentsGlutaryl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / SSGCID / GLUTARYL-COA DEHDROGENASE / MYCOBACERIUM SMEGMATIS / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / FADH2
Function / homology
Function and homology information


glutaryl-CoA dehydrogenase activity / glutaryl-CoA dehydrogenase (ETF) / fatty-acyl-CoA biosynthetic process / fatty acid beta-oxidation using acyl-CoA dehydrogenase / fatty-acyl-CoA binding / flavin adenine dinucleotide binding
Similarity search - Function
: / 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, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain ...: / 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, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA dehydrogenase/oxidase C-terminal / 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
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / Glutaryl-CoA dehydrogenase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionJul 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Sep 13, 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)176,72233
Polymers172,9514
Non-polymers3,77129
Water37,7772097
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27000 Å2
ΔGint-61 kcal/mol
Surface area44660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.670, 66.870, 167.460
Angle α, β, γ (deg.)90.00, 107.71, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Glutaryl-CoA dehydrogenase


Mass: 43237.805 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 7000084 / MC(2)155 / Gene: MSMEG_6686 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0R6V6, EC: 1.3.99.7
#2: Chemical
ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 15 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2097 / 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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 3350, 200MM POTASSIUM CITRATE TRIBASIC; MYSMA.01640.BA1, PW28880 AT 30.7 MG/ML; ADD 15% EG TO RESERVOIR FOR CRYO, PH N/A, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 11, 2011
RadiationMonochromator: Asymmetric curved crystal, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. all: 278810 / Num. obs: 276750 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 18.25 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 21.69
Reflection shellResolution: 1.45→1.49 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 3.2 / Num. unique all: 20619 / Rsym value: 0.309 / % possible all: 93.9

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
REFMAC5.5.0110refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2eba modified with CCP4 program CHAINSAW

2eba


Resolution: 1.45→45.48 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.668 / SU ML: 0.029 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.15 13939 5 %RANDOM
Rwork0.127 ---
all0.128 278810 --
obs0.128 276456 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å2-0 Å2-0.01 Å2
2--0.54 Å2-0 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.45→45.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11757 0 267 2097 14121
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02212610
X-RAY DIFFRACTIONr_bond_other_d0.0010.028552
X-RAY DIFFRACTIONr_angle_refined_deg1.511.99317170
X-RAY DIFFRACTIONr_angle_other_deg0.95320837
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.31751654
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.38823.761561
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.542152096
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.40215107
X-RAY DIFFRACTIONr_chiral_restr0.0950.21925
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214211
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022572
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_it0.7611.57804
X-RAY DIFFRACTIONr_mcbond_other0.2441.53242
X-RAY DIFFRACTIONr_mcangle_it1.288212501
X-RAY DIFFRACTIONr_scbond_it2.12134806
X-RAY DIFFRACTIONr_scangle_it3.3784.54613
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 996 -
Rwork0.227 18326 -
obs-19361 93.81 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.23510.03210.00030.088-0.02540.17120.0261-0.07-0.00310.0159-0.0109-0.00440.0326-0.0237-0.01520.0245-0.0301-0.01160.04930.01010.026330.023-12.76564.298
20.19820.0061-0.00240.18130.04960.28550.01350.06850-0.03220.0056-0.01870.03050.0432-0.01910.01560.0065-0.00340.0491-0.00680.016849.541-11.2217.815
30.2059-0.03590.04750.23320.03660.19890.0030.02150.0336-0.0245-0.01290.0197-0.018-0.05240.00990.00450.0032-0.00570.03940.00550.031419.8247.71228.988
40.28590.1130.10820.07670.03270.19150.0151-0.01590.00950.0141-0.002-0.00730.0050.0352-0.01310.0104-0.0124-0.00720.0412-0.01020.034763.2351.35655.631
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 396
2X-RAY DIFFRACTION2B11 - 396
3X-RAY DIFFRACTION3C11 - 396
4X-RAY DIFFRACTION4D11 - 396

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