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- PDB-5mzw: Crystal structure of the decarboxylase AibA/AibB -

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Basic information

Entry
Database: PDB / ID: 5mzw
TitleCrystal structure of the decarboxylase AibA/AibB
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 / Glutaconate CoA-transferase family, subunit B / Glutaconate CoA-transferase family, subunit A
Function and homology information
Biological speciesMyxococcus xanthus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.52 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 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)109,5747
Polymers109,2974
Non-polymers2763
Water22,0861226
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12610 Å2
ΔGint-69 kcal/mol
Surface area33370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.714, 93.600, 90.324
Angle α, β, γ (deg.)90.000, 104.320, 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: 26280.871 Da / Num. of mol.: 2 / Mutation: 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1226 / 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: 50.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH 5.0, 12 % PEG6000

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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: Apr 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.52→46.8 Å / Num. obs: 164999 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 9.06 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.061 / Rrim(I) all: 0.161 / Net I/σ(I): 12.1 / Num. measured all: 1140065 / Scaling rejects: 66
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.52-1.5570.830.8781100
8.33-46.870.0630.996199.5

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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: SAD / Resolution: 1.52→43.758 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.28
RfactorNum. reflection% reflection
Rfree0.1568 8293 5.03 %
Rwork0.1411 --
obs0.1419 164960 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 78.03 Å2 / Biso mean: 13.1808 Å2 / Biso min: 2.83 Å2
Refinement stepCycle: final / Resolution: 1.52→43.758 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7423 0 18 1226 8667
Biso mean--22.58 26.36 -
Num. residues----1006
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067733
X-RAY DIFFRACTIONf_angle_d0.85910601
X-RAY DIFFRACTIONf_chiral_restr0.0531255
X-RAY DIFFRACTIONf_plane_restr0.0071402
X-RAY DIFFRACTIONf_dihedral_angle_d9.964758
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
1.52-1.53730.20362760.175952385514
1.5373-1.55540.1792880.173351945482
1.5554-1.57430.20052730.169451945467
1.5743-1.59430.20022810.168851915472
1.5943-1.61520.17052730.170252325505
1.6152-1.63740.20082450.167252285473
1.6374-1.66080.1742850.158251805465
1.6608-1.68550.18672730.159551925465
1.6855-1.71190.19262900.155252355525
1.7119-1.740.16772850.151251745459
1.74-1.770.16012560.148752475503
1.77-1.80210.16752980.142251785476
1.8021-1.83680.16632700.148252065476
1.8368-1.87430.17592510.141552145465
1.8743-1.91510.15992690.139952245493
1.9151-1.95960.16442910.139352335524
1.9596-2.00860.15932660.138351915457
2.0086-2.06290.15712510.132952305481
2.0629-2.12360.16232740.1352355509
2.1236-2.19220.13652900.130551805470
2.1922-2.27050.15312840.126352145498
2.2705-2.36140.14122920.1352255517
2.3614-2.46890.13162970.129352205517
2.4689-2.5990.14432850.1352125497
2.599-2.76180.14672750.131452325507
2.7618-2.9750.15532830.130652095492
2.975-3.27430.14252460.137852795525
3.2743-3.74790.1272740.13752695543
3.7479-4.72110.14322910.126352665557
4.7211-43.77610.18032810.165853455626

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