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- PDB-5mzz: Crystal structure of the decarboxylase AibA/AibB in complex with ... -

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Basic information

Entry
Database: PDB / ID: 5mzz
TitleCrystal structure of the decarboxylase AibA/AibB in complex with 3-methylglutaconate
Components(Glutaconate CoA-transferase family, subunit ...) x 2
KeywordsLYASE / decarboxylase / CoA transferase like fold / 3-methylglutaconate
Function / homologyCoA-transferase activity / Coenzyme A transferase family I / Coenzyme A transferase / Coenzyme A transferase / NagB/RpiA transferase-like / 3-methylpent-2-enedioic acid / 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: 2.3 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)109,98011
Polymers109,2974
Non-polymers6837
Water6,630368
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13170 Å2
ΔGint-72 kcal/mol
Surface area33290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.962, 93.129, 90.798
Angle α, β, γ (deg.)90.000, 104.360, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Glutaconate CoA-transferase family, subunit ... , 2 types, 4 molecules ACDB

#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

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Non-polymers , 4 types, 375 molecules

#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: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-8EW / 3-methylpent-2-enedioic acid


Mass: 144.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H8O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / 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: 50.98 %
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 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→26.82 Å / Num. obs: 47619 / % possible obs: 99.1 % / Redundancy: 4.2 % / Biso Wilson estimate: 16.59 Å2 / CC1/2: 0.981 / Rmerge(I) obs: 0.178 / Rpim(I) all: 0.099 / Rrim(I) all: 0.204 / Net I/σ(I): 6.6 / Num. measured all: 200861 / Scaling rejects: 0
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.3-2.384.20.5380.829198
8.91-26.8240.0760.989195.8

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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: 2.3→26.82 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.91
RfactorNum. reflection% reflection
Rfree0.2072 2401 5.04 %
Rwork0.1788 --
obs0.1803 47602 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 63.74 Å2 / Biso mean: 20.3883 Å2 / Biso min: 9.39 Å2
Refinement stepCycle: final / Resolution: 2.3→26.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7435 0 49 369 7853
Biso mean--23.24 18.87 -
Num. residues----1006
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037721
X-RAY DIFFRACTIONf_angle_d0.56310563
X-RAY DIFFRACTIONf_chiral_restr0.0441244
X-RAY DIFFRACTIONf_plane_restr0.0041399
X-RAY DIFFRACTIONf_dihedral_angle_d11.3384730
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.34690.25461470.20612579272698
2.3469-2.39790.24021460.2132650279698
2.3979-2.45370.26341480.20532615276398
2.4537-2.5150.2531380.2032625276399
2.515-2.58290.23811520.20282632278499
2.5829-2.65890.23661220.19352674279699
2.6589-2.74460.22231470.19522612275999
2.7446-2.84260.23651530.18962632278599
2.8426-2.95630.22261440.19052661280599
2.9563-3.09060.21461210.18822689281099
3.0906-3.25330.1941250.192926812806100
3.2533-3.45680.24871270.183626842811100
3.4568-3.7230.17461520.176926872839100
3.723-4.09650.16551520.159126512803100
4.0965-4.68650.16791420.13826892831100
4.6865-5.89420.17561480.157626882836100
5.8942-26.82680.19641370.16042752288999

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