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- PDB-7bxq: 2-amino-3-ketobutyrate CoA ligase from Cupriavidus necator L-Thre... -

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Basic information

Entry
Database: PDB / ID: 7bxq
Title2-amino-3-ketobutyrate CoA ligase from Cupriavidus necator L-Threonine binding form
Components2-amino-3-ketobutyrate coenzyme A ligase
KeywordsLIGASE / TRANSFERASE / 2-amino-3-ketobutyrate CoA ligase / Cupriavidus necator
Function / homology
Function and homology information


glycine C-acetyltransferase / glycine C-acetyltransferase activity / L-threonine catabolic process to glycine / ligase activity / pyridoxal phosphate binding
Similarity search - Function
2-amino-3-ketobutyrate coenzyme A ligase / : / Aminotransferase, class-II, pyridoxal-phosphate binding site / Aminotransferases class-II pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Chem-2BK / 2-amino-3-ketobutyrate coenzyme A ligase
Similarity search - Component
Biological speciesCupriavidus necator (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsMotoyama, T. / Nakano, S. / Hasebe, F. / Miyoshi, N. / Ito, S.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18K14391 Japan
Japan Society for the Promotion of Science (JSPS)19J23697 Japan
CitationJournal: Commun Chem / Year: 2021
Title: Chemoenzymatic synthesis of 3-ethyl-2,5-dimethylpyrazine by L-threonine 3-dehydrogenase and 2-amino-3-ketobutyrate CoA ligase/L-threonine aldolase
Authors: Motoyama, T. / Nakano, S. / Hasebe, F. / Miyata, R. / Kumazawa, S. / Miyoshi, N. / Ito, S.
History
DepositionApr 20, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: 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: 2-amino-3-ketobutyrate coenzyme A ligase
B: 2-amino-3-ketobutyrate coenzyme A ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,2844
Polymers89,5832
Non-polymers7012
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9490 Å2
ΔGint-58 kcal/mol
Surface area26140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.708, 101.657, 69.854
Angle α, β, γ (deg.)90.000, 112.990, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein 2-amino-3-ketobutyrate coenzyme A ligase / AKB ligase / Glycine acetyltransferase


Mass: 44791.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus necator (bacteria) / Gene: kbl, H16_B0819 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0K313, glycine C-acetyltransferase
#2: Chemical ChemComp-2BK / N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-allothreonine


Mass: 350.262 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N2O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.14 Å3/Da / Density % sol: 42.65 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS pH 6.5, 25% w/v PEG3350, 3% w/v D-(+)-Glucose monohydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.49→49.9 Å / Num. obs: 26320 / % possible obs: 99.8 % / Redundancy: 10.2 % / Biso Wilson estimate: 38.21 Å2 / CC1/2: 0.998 / Net I/σ(I): 16.3
Reflection shellResolution: 2.49→2.58 Å / Num. unique obs: 3770 / CC1/2: 0.904

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FC4

1fc4


Resolution: 2.49→39.88 Å / SU ML: 0.3184 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.6829
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2577 1281 4.87 %
Rwork0.1851 25014 -
obs0.1885 26295 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.2 Å2
Refinement stepCycle: LAST / Resolution: 2.49→39.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6082 0 46 200 6328
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00746222
X-RAY DIFFRACTIONf_angle_d0.88688404
X-RAY DIFFRACTIONf_chiral_restr0.0524942
X-RAY DIFFRACTIONf_plane_restr0.00491112
X-RAY DIFFRACTIONf_dihedral_angle_d19.5349902
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.590.32011540.23642702X-RAY DIFFRACTION97.98
2.59-2.710.29551350.22612756X-RAY DIFFRACTION100
2.71-2.860.29351410.22642791X-RAY DIFFRACTION100
2.86-3.030.25941410.20212777X-RAY DIFFRACTION99.97
3.03-3.270.30251490.20752788X-RAY DIFFRACTION100
3.27-3.60.26591610.18552746X-RAY DIFFRACTION100
3.6-4.120.24861500.16492771X-RAY DIFFRACTION99.97
4.12-5.190.20231260.15452818X-RAY DIFFRACTION100
5.19-39.880.24411240.17682865X-RAY DIFFRACTION99.93

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