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- PDB-5n01: Crystal structure of the decarboxylase AibA/AibB C56N variant -

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Basic information

Entry
Database: PDB / ID: 5n01
TitleCrystal structure of the decarboxylase AibA/AibB C56N 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: 1.95 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)109,6489
Polymers109,3194
Non-polymers3285
Water20,3391129
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13310 Å2
ΔGint-74 kcal/mol
Surface area32590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.769, 93.217, 90.811
Angle α, β, γ (deg.)90.000, 104.340, 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: 26291.832 Da / Num. of mol.: 2 / Mutation: C56N, 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.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1129 / 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: 50.89 %
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: Jun 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.95→19.59 Å / Num. obs: 78188 / % possible obs: 99.5 % / Redundancy: 7.4 % / Biso Wilson estimate: 14.28 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.18 / Rpim(I) all: 0.07 / Rrim(I) all: 0.193 / Net I/σ(I): 10.3 / Num. measured all: 580152 / Scaling rejects: 3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.95-1.997.30.8170.796198.6
9.94-19.597.10.0460.998187.3

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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: 1.95→19.59 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.49
RfactorNum. reflection% reflection
Rfree0.1848 3939 5.04 %
Rwork0.155 --
obs0.1566 78158 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 78.68 Å2 / Biso mean: 18.2573 Å2 / Biso min: 5.87 Å2
Refinement stepCycle: final / Resolution: 1.95→19.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7412 0 22 1129 8563
Biso mean--22.84 26.15 -
Num. residues----1004
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047682
X-RAY DIFFRACTIONf_angle_d0.69710521
X-RAY DIFFRACTIONf_chiral_restr0.0461247
X-RAY DIFFRACTIONf_plane_restr0.0051393
X-RAY DIFFRACTIONf_dihedral_angle_d10.2334703
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-1.97380.23331530.19532649280299
1.9738-1.99870.22281240.18892600272499
1.9987-2.0250.22991440.19242645278998
2.025-2.05270.26521280.18582601272999
2.0527-2.0820.24051090.17512646275599
2.082-2.11310.19291450.17242616276199
2.1131-2.1460.19531430.17342629277299
2.146-2.18120.19441390.16522610274999
2.1812-2.21870.19921490.17092642279199
2.2187-2.2590.20271420.165626252767100
2.259-2.30240.20141510.162226432794100
2.3024-2.34930.20141480.16462606275499
2.3493-2.40030.19651440.160826702814100
2.4003-2.45610.19121570.158126472804100
2.4561-2.51740.21531370.16726392776100
2.5174-2.58530.22521480.154326392787100
2.5853-2.66120.1891280.156227062834100
2.6612-2.74690.18361460.153726232769100
2.7469-2.84470.18471530.150226392792100
2.8447-2.95830.17651460.150426692815100
2.9583-3.09240.17821210.151826842805100
3.0924-3.25480.17471240.154926752799100
3.2548-3.45760.1871260.15126922818100
3.4576-3.72290.15711530.146326682821100
3.7229-4.09450.14271500.131926452795100
4.0945-4.67990.14241430.122126842827100
4.6799-5.86980.16041450.142326902835100
5.8698-19.59160.19481430.152127372880100

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