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- PDB-2oku: The crystal structure of the acyl-CoA dehydrogenase family protei... -

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Basic information

Entry
Database: PDB / ID: 2oku
TitleThe crystal structure of the acyl-CoA dehydrogenase family protein from Porphyromonas gingivalis
ComponentsAcyl-CoA dehydrogenase family protein
KeywordsOXIDOREDUCTASE / The acyl-CoA dehydrogenase / Porphyromonas gingivalis / PSI-2 / MCSG / Structural Genomics / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


acyl-CoA dehydrogenase activity / flavin adenine dinucleotide binding
Similarity search - Function
Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, C-terminal / Acyl-CoA dehydrogenase, C-terminal domain superfamily / Acyl-CoA dehydrogenase C terminal / Broad-specificity linear acyl-CoA dehydrogenase FadE5-like / Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, C-terminal domain ...Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, C-terminal / Acyl-CoA dehydrogenase, C-terminal domain superfamily / Acyl-CoA dehydrogenase C terminal / Broad-specificity linear acyl-CoA dehydrogenase FadE5-like / Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / 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 / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Acyl-CoA dehydrogenase family protein
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsZhang, R. / Bigelow, L. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the acyl-CoA dehydrogenase family protein from Porphyromonas gingivalis
Authors: Zhang, R. / Bigelow, L. / Abdullah, J. / Joachimiak, A.
History
DepositionJan 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Acyl-CoA dehydrogenase family protein
B: Acyl-CoA dehydrogenase family protein


Theoretical massNumber of molelcules
Total (without water)30,9322
Polymers30,9322
Non-polymers00
Water6,341352
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-16 kcal/mol
Surface area12490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.340, 90.340, 102.069
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThis protein existed as dimer. The deposited structure represents the dimer in the asymmetric unit.

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Components

#1: Protein Acyl-CoA dehydrogenase family protein


Mass: 15465.808 Da / Num. of mol.: 2 / Fragment: C-terminal domain, residues 443-573
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Strain: W83 / Gene: PG_0775 / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q7MW70
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 352 / 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: 3.37 Å3/Da / Density % sol: 63.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.26M (NH4)2SO4, 0.1M Tris-HCl, 0.2M LiSO4, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 18, 2006 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.9→67.57 Å / Num. all: 32189 / Num. obs: 32154 / % possible obs: 99.89 % / Observed criterion σ(I): 2 / Redundancy: 18.9 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 31.53
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 17.4 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.27 / Num. unique all: 2461 / % possible all: 99.15

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→67.57 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.819 / SU ML: 0.061 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.106 / ESU R Free: 0.106
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20541 1716 5.1 %RANDOM
Rwork0.17345 ---
all0.17498 32154 --
obs0.17498 32154 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.476 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2--0.31 Å20 Å2
3----0.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.042 Å0.032 Å
Luzzati d res low-6 Å
Luzzati sigma a0.5 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 1.9→67.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1937 0 0 352 2289
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221979
X-RAY DIFFRACTIONr_bond_other_d0.0010.021368
X-RAY DIFFRACTIONr_angle_refined_deg1.3421.9542670
X-RAY DIFFRACTIONr_angle_other_deg1.41333299
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4515238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.40423.455110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.53515359
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2991523
X-RAY DIFFRACTIONr_chiral_restr0.1460.2296
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022217
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02426
X-RAY DIFFRACTIONr_nbd_refined0.2310.2512
X-RAY DIFFRACTIONr_nbd_other0.1840.21485
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2990
X-RAY DIFFRACTIONr_nbtor_other0.0870.2999
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2246
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.120.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3360.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2530.233
X-RAY DIFFRACTIONr_mcbond_it1.5281.51527
X-RAY DIFFRACTIONr_mcbond_other0.2441.5476
X-RAY DIFFRACTIONr_mcangle_it1.38221919
X-RAY DIFFRACTIONr_scbond_it3.123870
X-RAY DIFFRACTIONr_scangle_it4.2134.5751
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 109 -
Rwork0.225 2331 -
obs-2331 99.15 %
Refinement TLS params.Method: refined / Origin x: 32.63 Å / Origin y: -6.657 Å / Origin z: -4.34 Å
111213212223313233
T-0.0004 Å20.0059 Å20.0023 Å2--0.0277 Å2-0.0167 Å2---0.071 Å2
L0.8348 °20.5781 °20.2999 °2-0.9875 °20.1925 °2--0.7317 °2
S0.0427 Å °-0.0698 Å °0.0104 Å °0.0033 Å °-0.0909 Å °0.0266 Å °0.101 Å °-0.0478 Å °0.0482 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA443 - 4801 - 38
2X-RAY DIFFRACTION1AA481 - 52039 - 78
3X-RAY DIFFRACTION1AA521 - 56479 - 122
4X-RAY DIFFRACTION1BB445 - 4803 - 38
5X-RAY DIFFRACTION1BB481 - 52039 - 78
6X-RAY DIFFRACTION1BB521 - 56079 - 118

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