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- PDB-5n03: Crystal structure of the decarboxylase AibA/AibB C56V variant -

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Basic information

Entry
Database: PDB / ID: 5n03
TitleCrystal structure of the decarboxylase AibA/AibB C56V 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 / FOURIER SYNTHESIS / Resolution: 2.1 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)109,4677
Polymers109,2894
Non-polymers1773
Water17,781987
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12810 Å2
ΔGint-72 kcal/mol
Surface area32870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.999, 93.246, 91.061
Angle α, β, γ (deg.)90.000, 104.410, 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: 26276.859 Da / Num. of mol.: 2 / Mutation: C56V, 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.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 987 / 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: 2.51 Å3/Da / Density % sol: 51.05 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.05→19.54 Å / Num. obs: 67504 / % possible obs: 99.2 % / Redundancy: 4.2 % / Biso Wilson estimate: 11.74 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.09 / Rrim(I) all: 0.187 / Net I/σ(I): 9.8 / Num. measured all: 284760 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.05-2.13.30.5081379142150.7120.3310.6122.692.1
9.62-19.544.10.03125196070.9990.0180.0364788.1

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimless0.1.29data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5MZW

5mzw


Resolution: 2.1→19.536 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1983 3206 5.08 %
Rwork0.1661 59899 -
obs0.1678 63105 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.24 Å2 / Biso mean: 13.7851 Å2 / Biso min: 1.56 Å2
Refinement stepCycle: final / Resolution: 2.1→19.536 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7399 0 12 987 8398
Biso mean--12.78 22.13 -
Num. residues----1005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027664
X-RAY DIFFRACTIONf_angle_d0.54310498
X-RAY DIFFRACTIONf_chiral_restr0.0421245
X-RAY DIFFRACTIONf_plane_restr0.0041391
X-RAY DIFFRACTIONf_dihedral_angle_d11.8674687
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.13130.2531250.20012559268499
2.1313-2.16460.23431530.189425992752100
2.1646-2.20.22981440.18962554269899
2.2-2.23790.21011210.185226142735100
2.2379-2.27850.24161470.18062562270999
2.2785-2.32230.24071460.187525992745100
2.3223-2.36960.21681510.187825662717100
2.3696-2.42110.2081580.182125702728100
2.4211-2.47730.24381360.183826132749100
2.4773-2.53910.24671390.18525922731100
2.5391-2.60760.2211420.171126332775100
2.6076-2.68410.19641260.172525902716100
2.6841-2.77050.221460.180626032749100
2.7705-2.86930.19661340.167325942728100
2.8693-2.98380.20021520.168625742726100
2.9838-3.11910.18191190.16526542773100
3.1191-3.28280.18151190.168626132732100
3.2828-3.48740.22741240.162326592783100
3.4874-3.75490.1741510.157125942745100
3.7549-4.12950.15431530.135926162769100
4.1295-4.71970.14821390.125226232762100
4.7197-5.91870.16351420.153226312773100
5.9187-19.53650.17931390.15326872826100

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