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

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Basic information

Entry
Database: PDB / ID: 5mzy
TitleCrystal structure of the decarboxylase AibA/AibB in complex with a possible transition state analog
Components(Glutaconate CoA-transferase family, subunit ...) x 2
KeywordsLYASE / decarboxylase / CoA transferase like fold / transition state analog
Function / homologyCoA-transferase activity / Coenzyme A transferase family I / Coenzyme A transferase / Coenzyme A transferase / NagB/RpiA transferase-like / Chem-8EZ / 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: 1.6 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)110,06812
Polymers109,2974
Non-polymers7718
Water15,979887
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13660 Å2
ΔGint-74 kcal/mol
Surface area33290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.940, 93.368, 90.660
Angle α, β, γ (deg.)90.000, 104.280, 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, 895 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / 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-8EZ / (1~{R},2~{S})-2-methylcyclohexane-1-carboxylic acid


Mass: 142.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H14O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 887 / 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: 50.88 %
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: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.6→41.94 Å / Num. obs: 142059 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 13.47 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.041 / Rrim(I) all: 0.106 / Net I/σ(I): 14.4 / Num. measured all: 929533 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
1.6-1.636.70.6530.8640.270.708100
8.76-41.946.60.0320.9990.0130.03598.8

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5MZW

5mzw


Resolution: 1.6→41.94 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.33
RfactorNum. reflection% reflection
Rfree0.1629 7125 5.02 %
Rwork0.1436 --
obs0.1446 142008 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.39 Å2 / Biso mean: 18.0153 Å2 / Biso min: 5.39 Å2
Refinement stepCycle: final / Resolution: 1.6→41.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7455 0 81 887 8423
Biso mean--27.59 27.29 -
Num. residues----1010
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087818
X-RAY DIFFRACTIONf_angle_d0.98810707
X-RAY DIFFRACTIONf_chiral_restr0.0591266
X-RAY DIFFRACTIONf_plane_restr0.0081414
X-RAY DIFFRACTIONf_dihedral_angle_d11.3874817
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.61820.23532360.200145044740100
1.6182-1.63720.21952070.192844594666100
1.6372-1.65720.2122270.181844494676100
1.6572-1.67820.23292480.177345484796100
1.6782-1.70030.21142370.171744514688100
1.7003-1.72350.20032610.166944444705100
1.7235-1.74820.19442380.163344624700100
1.7482-1.77430.18662250.155545524777100
1.7743-1.8020.17822480.152144544702100
1.802-1.83150.19242440.153344964740100
1.8315-1.86310.19862180.151944954713100
1.8631-1.8970.16732320.150544644696100
1.897-1.93350.20222290.16354463469299
1.9335-1.97290.17322490.152745354784100
1.9729-2.01580.15092290.137744764705100
2.0158-2.06270.18432240.142844904714100
2.0627-2.11430.19142270.138545044731100
2.1143-2.17150.15212540.13244994753100
2.1715-2.23540.13782240.133145004724100
2.2354-2.30750.1762640.138544374701100
2.3075-2.390.14322480.126645224770100
2.39-2.48570.13092520.126344474699100
2.4857-2.59880.15252450.12545434788100
2.5988-2.73580.14512280.134344794707100
2.7358-2.90710.15862510.130145084759100
2.9071-3.13150.14452290.139145004729100
3.1315-3.44650.16752050.14545544759100
3.4465-3.94490.14742570.141745304787100
3.9449-4.96890.12632480.124245074755100
4.9689-41.95920.17652410.166446114852100

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