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- PDB-5n00: Crystal structure of the decarboxylase AibA/AibB C56A variant -

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Basic information

Entry
Database: PDB / ID: 5n00
TitleCrystal structure of the decarboxylase AibA/AibB C56A 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
C: Glutaconate CoA-transferase family, subunit A
A: Glutaconate CoA-transferase family, subunit A
B: Glutaconate CoA-transferase family, subunit B
D: Glutaconate CoA-transferase family, subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,2925
Polymers109,2334
Non-polymers591
Water17,619978
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12340 Å2
ΔGint-68 kcal/mol
Surface area33370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.947, 93.482, 90.846
Angle α, β, γ (deg.)90.000, 104.490, 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: 26248.807 Da / Num. of mol.: 2 / Mutation: C56A, 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.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 978 / 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: 2.52 Å3/Da / Density % sol: 51.18 %
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: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→46.88 Å / Num. obs: 85333 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 18.49 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.047 / Rrim(I) all: 0.12 / Net I/σ(I): 11 / Num. measured all: 545067 / Scaling rejects: 0
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.9-1.935.10.6330.794199.9
10.05-46.885.90.0490.999198.8

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Processing

Software
NameVersionClassification
Aimless0.1.29data 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→46.88 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.94
RfactorNum. reflection% reflection
Rfree0.1854 4303 5.04 %
Rwork0.1498 --
obs0.1516 85297 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 97.31 Å2 / Biso mean: 22.569 Å2 / Biso min: 7.83 Å2
Refinement stepCycle: final / Resolution: 1.9→46.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7410 0 7 978 8395
Biso mean--27.01 31.22 -
Num. residues----1005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057672
X-RAY DIFFRACTIONf_angle_d0.7710513
X-RAY DIFFRACTIONf_chiral_restr0.0491249
X-RAY DIFFRACTIONf_plane_restr0.0061390
X-RAY DIFFRACTIONf_dihedral_angle_d9.8964704
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
1.9-1.92160.29081420.232727162858
1.9216-1.94420.25491480.218627122860
1.9442-1.96790.24561460.195626782824
1.9679-1.99280.23191410.181226712812
1.9928-2.01910.21531390.171927082847
2.0191-2.04670.22521490.169426662815
2.0467-2.0760.2411970.161327182815
2.076-2.1070.2021540.154126812835
2.107-2.13990.20541470.153426672814
2.1399-2.1750.18321520.152327302882
2.175-2.21250.1971430.148226802823
2.2125-2.25270.18631410.143726802821
2.2527-2.2960.22661500.145826782828
2.296-2.34290.18761610.14626662827
2.3429-2.39380.21481430.147927242867
2.3938-2.44950.16041560.13926542810
2.4495-2.51080.19991370.147926992836
2.5108-2.57860.19771600.143526862846
2.5786-2.65450.19161230.138227052828
2.6545-2.74020.19091470.150326882835
2.7402-2.83810.18871620.146126892851
2.8381-2.95170.19641380.145426982836
2.9517-3.0860.16851310.155927212852
3.086-3.24870.16791270.151527052832
3.2487-3.45220.21111230.14927292852
3.4522-3.71860.15341560.145227222878
3.7186-4.09270.1481530.129326982851
4.0927-4.68440.14471450.118527222867
4.6844-5.90.15821490.147827232872
5.9-46.89410.19871430.166127802923

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