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- PDB-7bxr: 2-amino-3-ketobutyrate CoA ligase from Cupriavidus necator 3-Hydr... -

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Basic information

Entry
Database: PDB / ID: 7bxr
Title2-amino-3-ketobutyrate CoA ligase from Cupriavidus necator 3-Hydroxynorvaline 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-F9X / 2-amino-3-ketobutyrate coenzyme A ligase
Similarity search - Component
Biological speciesCupriavidus necator (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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)90,3124
Polymers89,5832
Non-polymers7292
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9510 Å2
ΔGint-54 kcal/mol
Surface area26130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.728, 101.703, 69.780
Angle α, β, γ (deg.)90.000, 112.911, 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-F9X / (2S,3R)-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]-3-oxidanyl-pentanoic acid


Mass: 364.288 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H21N2O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 42.67 %
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 PEG 3350, 3% w/v D-Sorbitol

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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: 2.55→47.8 Å / Num. obs: 24744 / % possible obs: 99.7 % / Redundancy: 6.9 % / Biso Wilson estimate: 35.4 Å2 / CC1/2: 0.996 / Net I/σ(I): 13.1
Reflection shellResolution: 2.55→2.64 Å / Num. unique obs: 3571 / CC1/2: 0.856

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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: 2.55→47.76 Å / SU ML: 0.3495 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.653
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2696 1196 4.84 %
Rwork0.1841 23525 -
obs0.188 24721 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.86 Å2
Refinement stepCycle: LAST / Resolution: 2.55→47.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6082 0 48 215 6345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076224
X-RAY DIFFRACTIONf_angle_d0.91688406
X-RAY DIFFRACTIONf_chiral_restr0.0515942
X-RAY DIFFRACTIONf_plane_restr0.00471112
X-RAY DIFFRACTIONf_dihedral_angle_d14.7255904
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.650.32561190.23042560X-RAY DIFFRACTION98.17
2.65-2.770.31571350.23492598X-RAY DIFFRACTION99.53
2.77-2.910.31131320.2292597X-RAY DIFFRACTION99.56
2.91-3.10.29291550.20972599X-RAY DIFFRACTION99.67
3.1-3.330.30591340.20322597X-RAY DIFFRACTION99.78
3.34-3.670.26391380.17772625X-RAY DIFFRACTION99.89
3.67-4.20.22921450.1582609X-RAY DIFFRACTION99.93
4.2-5.290.24591160.15352649X-RAY DIFFRACTION100
5.29-47.760.24791220.17492691X-RAY DIFFRACTION99.89

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