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- PDB-5n02: Crystal structure of the decarboxylase AibA/AibB C56S variant -

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Basic information

Entry
Database: PDB / ID: 5n02
TitleCrystal structure of the decarboxylase AibA/AibB C56S variant
Components
  • Glutaconate CoA-transferase family, subunit A
  • Glutaconate CoA-transferase family, subunit B
KeywordsLYASE / decarboxylase / CoA transferase like fold
Function / homologyCoA-transferase activity / Coenzyme A transferase family I / Coenzyme A transferase / Coenzyme A transferase / NagB/RpiA transferase-like / ACETATE ION / Glutaconate CoA-transferase family, subunit B / Glutaconate CoA-transferase family, subunit A
Function and homology information
Biological speciesMyxococcus xanthus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsBock, T. / Luxenburger, E. / Hoffmann, J. / Schuetza, V. / Feiler, C. / Mueller, R. / Blankenfeldt, W.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: AibA/AibB Induces an Intramolecular Decarboxylation in Isovalerate Biosynthesis by Myxococcus xanthus.
Authors: Bock, T. / Luxenburger, E. / Hoffmann, J. / Schutza, V. / Feiler, C. / Muller, R. / Blankenfeldt, W.
History
DepositionFeb 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: 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: Glutaconate CoA-transferase family, subunit A
C: Glutaconate CoA-transferase family, subunit A
D: Glutaconate CoA-transferase family, subunit B
B: Glutaconate CoA-transferase family, subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,3836
Polymers109,2654
Non-polymers1182
Water18,1231006
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12550 Å2
ΔGint-69 kcal/mol
Surface area33250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.565, 93.754, 90.204
Angle α, β, γ (deg.)90.000, 104.210, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glutaconate CoA-transferase family, subunit A


Mass: 28367.838 Da / Num. of mol.: 2 / Mutation: K191A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxococcus xanthus (strain DK 1622) (bacteria)
Strain: DK 1622 / Gene: MXAN_4264 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1D4I4
#2: Protein Glutaconate CoA-transferase family, subunit B


Mass: 26264.807 Da / Num. of mol.: 2 / Mutation: C56S, E200A, E201A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxococcus xanthus (strain DK 1622) (bacteria)
Strain: DK 1622 / Gene: MXAN_4265 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1D4I3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1006 / 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: 2.5 Å3/Da / Density % sol: 50.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.085 M sodium acetate, 0.17 M ammonium acetate, 15 % glycerol, 25 % PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.9→46.88 Å / Num. obs: 84539 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 17.57 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.044 / Rrim(I) all: 0.117 / Net I/σ(I): 13.6 / Num. measured all: 582277 / Scaling rejects: 0
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.9-1.9370.6110.833199.7
10.05-46.886.50.0290.999198.5

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Processing

Software
NameVersionClassification
Aimless0.3.5data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5MZW

5mzw


Resolution: 1.9→46.73 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 15.94
RfactorNum. reflection% reflection
Rfree0.1725 4266 5.05 %
Rwork0.1428 --
obs0.1443 84510 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 90.24 Å2 / Biso mean: 21.8865 Å2 / Biso min: 8.93 Å2
Refinement stepCycle: final / Resolution: 1.9→46.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7428 0 11 1006 8445
Biso mean--29.88 30.11 -
Num. residues----1006
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057677
X-RAY DIFFRACTIONf_angle_d0.75710513
X-RAY DIFFRACTIONf_chiral_restr0.0491246
X-RAY DIFFRACTIONf_plane_restr0.0061391
X-RAY DIFFRACTIONf_dihedral_angle_d10.0484700
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9-1.92160.24321410.186226742815
1.9216-1.94420.23531520.183226312783
1.9442-1.96790.21011420.176226492791
1.9679-1.99280.21151370.164226802817
1.9928-2.0190.20461480.163526752823
2.019-2.04670.20391260.15626592785
2.0467-2.07590.22381120.152826892801
2.0759-2.10690.19141490.150126432792
2.1069-2.13990.19711420.145426922834
2.1399-2.17490.17071470.144226402787
2.1749-2.21240.16081490.139126612810
2.2124-2.25270.17711420.129426702812
2.2527-2.2960.21021480.135726752823
2.296-2.34290.16151570.132926302787
2.3429-2.39380.17541400.133226982838
2.3938-2.44950.14571580.125926492807
2.4495-2.51070.19351380.133626622800
2.5107-2.57860.17261520.135426542806
2.5786-2.65450.17931310.132427272858
2.6545-2.74020.18161450.140526342779
2.7402-2.83810.18661510.132926682819
2.8381-2.95170.17361420.138926752817
2.9517-3.0860.16561260.147826962822
3.086-3.24870.16431300.146226962826
3.2487-3.45210.16791240.145927082832
3.4521-3.71860.16181520.145126792831
3.7186-4.09260.14661570.131726742831
4.0926-4.68430.12941410.118927002841
4.6843-5.89990.14921460.147127042850
5.8999-46.74370.1921410.162827522893

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