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- PDB-6ijc: Structure of MMPA-CoA dehydrogenase from Roseovarius nubinhibens ISM -

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Basic information

Entry
Database: PDB / ID: 6ijc
TitleStructure of MMPA-CoA dehydrogenase from Roseovarius nubinhibens ISM
ComponentsAcyl-CoA dehydrogenase family protein
KeywordsOXIDOREDUCTASE / Short-chain acyl CoA dehydrogenase / FAD / redox reaction
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-CH group of donors / flavin adenine dinucleotide binding
Similarity search - Function
Acetyl-CoA dehydrogenase-like C-terminal domain / Acetyl-CoA dehydrogenase C-terminal like / 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
Similarity search - Domain/homology
Acyl-CoA dehydrogenase family protein
Similarity search - Component
Biological speciesRoseovarius nubinhibens ISM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsShao, X. / Yuan, Z.L. / Cao, H.Y. / Wang, P. / Li, C.Y. / Chen, X.L. / Zhang, Y.Z.
Funding support China, 3items
OrganizationGrant numberCountry
National Science Foundation (China)31630012 China
National Science Foundation (China)41706152 China
National Science Foundation (China)31728001 China
CitationJournal: Mol.Microbiol. / Year: 2019
Title: Mechanistic insight into 3-methylmercaptopropionate metabolism and kinetical regulation of demethylation pathway in marine dimethylsulfoniopropionate-catabolizing bacteria.
Authors: Shao, X. / Cao, H.Y. / Zhao, F. / Peng, M. / Wang, P. / Li, C.Y. / Shi, W.L. / Wei, T.D. / Yuan, Z. / Zhang, X.H. / Chen, X.L. / Todd, J.D. / Zhang, Y.Z.
History
DepositionOct 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,8183
Polymers128,5362
Non-polymers2821
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint-18 kcal/mol
Surface area40260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.012, 103.429, 125.963
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 Acyl-CoA dehydrogenase family protein / MMPA-CoA dehydrogenase


Mass: 64267.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Roseovarius nubinhibens ISM (bacteria) / Strain: ISM / Gene: dmdC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A3SI50
#2: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 2.05 Å3/Da / Density % sol: 40.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Bis-Tris propane, PEG 3350, Sodium nitrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.3→39.97 Å / Num. obs: 47323 / % possible obs: 99.4 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 19.07
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.478

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y9J

4y9j


Resolution: 2.3→39.97 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.75
RfactorNum. reflection% reflection
Rfree0.2259 2390 5.05 %
Rwork0.1747 --
obs0.1774 47305 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→39.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8550 0 19 292 8861
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088744
X-RAY DIFFRACTIONf_angle_d0.89311791
X-RAY DIFFRACTIONf_dihedral_angle_d15.485212
X-RAY DIFFRACTIONf_chiral_restr0.0491254
X-RAY DIFFRACTIONf_plane_restr0.0061558
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2971-2.3440.23961120.19312341X-RAY DIFFRACTION89
2.344-2.3950.27861330.19032621X-RAY DIFFRACTION99
2.395-2.45070.25731450.18952613X-RAY DIFFRACTION99
2.4507-2.51190.25471270.19152620X-RAY DIFFRACTION99
2.5119-2.57980.26791330.18092648X-RAY DIFFRACTION99
2.5798-2.65570.24111480.18372595X-RAY DIFFRACTION100
2.6557-2.74150.26911550.1872640X-RAY DIFFRACTION99
2.7415-2.83940.24391260.18592651X-RAY DIFFRACTION100
2.8394-2.95310.25011370.1942638X-RAY DIFFRACTION99
2.9531-3.08740.30231500.19192626X-RAY DIFFRACTION100
3.0874-3.25010.2691590.18942663X-RAY DIFFRACTION99
3.2501-3.45370.23291310.1772652X-RAY DIFFRACTION100
3.4537-3.72010.20841350.16842682X-RAY DIFFRACTION99
3.7201-4.09420.17721470.15622658X-RAY DIFFRACTION99
4.0942-4.68590.21061220.1522711X-RAY DIFFRACTION99
4.6859-5.90080.22691580.17092719X-RAY DIFFRACTION100
5.9008-40.51230.18241720.17192837X-RAY DIFFRACTION100

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