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- PDB-6es9: Methylsuccinyl-CoA dehydrogenase of Paracoccus denitrificans with... -

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Basic information

Entry
Database: PDB / ID: 6es9
TitleMethylsuccinyl-CoA dehydrogenase of Paracoccus denitrificans with bound flavin adenine dinucleotide
ComponentsAcyl-CoA dehydrogenase
KeywordsFLAVOPROTEIN / methylsuccinyl-CoA / acyl-CoA dehydrogenase / flavin adenine dinucleotide / ethylmalonyl-CoA pathway
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-CH group of donors; With a flavin as acceptor / acyl-CoA dehydrogenase activity / flavin adenine dinucleotide binding
Similarity search - Function
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
Similarity search - Domain/homology
COENZYME A / FLAVIN-ADENINE DINUCLEOTIDE / Acyl-CoA dehydrogenase
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.37 Å
AuthorsZarzycki, J. / Schwander, T. / Erb, T.J.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural basis for substrate specificity of methylsuccinyl-CoA dehydrogenase, an unusual member of the acyl-CoA dehydrogenase family.
Authors: Schwander, T. / McLean, R. / Zarzycki, J. / Erb, T.J.
History
DepositionOct 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 3, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Jul 13, 2022Group: Database references / Structure summary / Category: audit_author / database_2
Item: _audit_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jan 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acyl-CoA dehydrogenase
B: Acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,46110
Polymers119,9702
Non-polymers3,4908
Water25,0231389
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10670 Å2
ΔGint-77 kcal/mol
Surface area38070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.596, 105.193, 138.939
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 Acyl-CoA dehydrogenase /


Mass: 59985.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (strain Pd 1222) (bacteria)
Strain: Pd 1222 / Gene: Pden_2840 / Plasmid: pTE849 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A1B5Y0, Oxidoreductases; Acting on the CH-CH group of donors; With a flavin as acceptor
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1389 / 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: 2.49 Å3/Da / Density % sol: 50.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1 part protein solution (20.0 mg/mL in 20 mM Tris-HCl, pH 7.9, 200 mM sodium chloride, 1.5 mM FAD, 3 mM mesaconyl-CoA) + 1 part buffer (0.1 M Tris-HCl, pH 8.0, 30% w/v PEG5000 MME, 200 mM lithium sulfate)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979026 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979026 Å / Relative weight: 1
ReflectionResolution: 1.37→17.573 Å / Num. obs: 249985 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 15.84 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.026 / Rrim(I) all: 0.07 / Rsym value: 0.065 / Net I/av σ(I): 7.7 / Net I/σ(I): 15.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym value% possible all
1.37-1.447.41.1031.6362410.6320.4361.1871.103100
4.33-17.5737.10.02853.182520.9990.0110.030.02898.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALAdata scaling
TRUNCATEdata reduction
PHASERphasing
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N5F

4n5f


Resolution: 1.37→17.573 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.44
RfactorNum. reflection% reflection
Rfree0.1847 2000 0.8 %
Rwork0.176 --
obs0.176 249828 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 71.5 Å2 / Biso mean: 22.0831 Å2 / Biso min: 8.82 Å2
Refinement stepCycle: final / Resolution: 1.37→17.573 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8328 0 180 1389 9897
Biso mean--23.23 31.31 -
Num. residues----1090
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0168725
X-RAY DIFFRACTIONf_angle_d1.40511848
X-RAY DIFFRACTIONf_chiral_restr0.0981298
X-RAY DIFFRACTIONf_plane_restr0.011535
X-RAY DIFFRACTIONf_dihedral_angle_d20.5163184
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.37-1.40420.28321420.27551760417746
1.4042-1.44220.2621410.25471749317634
1.4422-1.48460.25631420.22671758017722
1.4846-1.53250.19551420.20191756517707
1.5325-1.58720.20511420.18581756417706
1.5872-1.65080.16761420.17041758217724
1.6508-1.72580.1931420.16481766617808
1.7258-1.81670.17561420.15941765317795
1.8167-1.93040.19481420.15991761817760
1.9304-2.07920.17041440.1681770317847
2.0792-2.28810.19031420.1711773817880
2.2881-2.61820.18421450.18141779317938
2.6182-3.29510.18571440.17651793018074
3.2951-17.57430.16561480.16581833918487
Refinement TLS params.Method: refined / Origin x: 9.0776 Å / Origin y: 0.3976 Å / Origin z: -14.9819 Å
111213212223313233
T0.1 Å2-0.0012 Å20.0039 Å2-0.1013 Å2-0.0024 Å2--0.1373 Å2
L0.1067 °20.0334 °2-0.0205 °2-0.1704 °20.034 °2--0.4125 °2
S0.0063 Å °0.0036 Å °0.033 Å °0.0024 Å °0.0081 Å °0.0133 Å °-0.0081 Å °-0.0392 Å °-0.0142 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA27 - 600
2X-RAY DIFFRACTION1allB27 - 600
3X-RAY DIFFRACTION1allS1 - 1389

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