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- PDB-7bxs: 2-amino-3-ketobutyrate CoA ligase from Cupriavidus necator glycin... -

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Basic information

Entry
Database: PDB / ID: 7bxs
Title2-amino-3-ketobutyrate CoA ligase from Cupriavidus necator glycine 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 / biosynthetic process / 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-PLG / 2-amino-3-ketobutyrate coenzyme A ligase
Similarity search - Component
Biological speciesCupriavidus necator (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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)90,1964
Polymers89,5832
Non-polymers6122
Water5,224290
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9510 Å2
ΔGint-58 kcal/mol
Surface area26060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.692, 101.802, 69.832
Angle α, β, γ (deg.)90.000, 112.983, 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-PLG / N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] / N-PYRIDOXYL-GLYCINE-5-MONOPHOSPHATE


Mass: 306.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N2O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 2.15 Å3/Da / Density % sol: 42.7 %
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 Dextran sulfate sodium salt (Mr 5000)

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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: 2.5→47.73 Å / Num. obs: 26198 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 32.67 Å2 / CC1/2: 0.997 / Net I/σ(I): 15.5
Reflection shellResolution: 2.5→2.59 Å / Num. unique obs: 3804 / CC1/2: 0.9

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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: 2.5→47.73 Å / SU ML: 0.3352 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.2866
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2273 1272 4.86 %
Rwork0.1685 24902 -
obs0.1713 26174 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.18 Å2
Refinement stepCycle: LAST / Resolution: 2.5→47.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6082 0 40 290 6412
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00726216
X-RAY DIFFRACTIONf_angle_d0.88628394
X-RAY DIFFRACTIONf_chiral_restr0.0515938
X-RAY DIFFRACTIONf_plane_restr0.00441112
X-RAY DIFFRACTIONf_dihedral_angle_d17.4101900
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.60.33321540.23062714X-RAY DIFFRACTION99.65
2.6-2.720.25041280.20572760X-RAY DIFFRACTION100
2.72-2.860.27611450.19472785X-RAY DIFFRACTION100
2.86-3.040.24291370.18812755X-RAY DIFFRACTION99.97
3.04-3.280.28181500.18622761X-RAY DIFFRACTION100
3.28-3.610.23631620.16692729X-RAY DIFFRACTION100
3.61-4.130.18991490.14192764X-RAY DIFFRACTION100
4.13-5.20.16931240.13652789X-RAY DIFFRACTION100
5.2-47.730.20621230.16772845X-RAY DIFFRACTION99.87

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