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- PDB-1fc4: 2-AMINO-3-KETOBUTYRATE COA LIGASE -

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Basic information

Entry
Database: PDB / ID: 1fc4
Title2-AMINO-3-KETOBUTYRATE COA LIGASE
Components2-AMINO-3-KETOBUTYRATE CONENZYME A LIGASE
KeywordsTRANSFERASE / 2-amino-3-ketobutyrate CoA ligase / pyridoxal phosphate / coenzyme A / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI
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 / metal ion binding / cytoplasm / cytosol
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 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain ...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 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-AMINO-3-KETOBUTYRIC ACID / PYRIDOXAL-5'-PHOSPHATE / 2-amino-3-ketobutyrate coenzyme A ligase / 2-amino-3-ketobutyrate coenzyme A ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsSchmidt, A. / Matte, A. / Li, Y. / Sivaraman, J. / Larocque, R. / Schrag, J.D. / Smith, C. / Sauve, V. / Cygler, M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: Biochemistry / Year: 2001
Title: Three-dimensional structure of 2-amino-3-ketobutyrate CoA ligase from Escherichia coli complexed with a PLP-substrate intermediate: inferred reaction mechanism.
Authors: Schmidt, A. / Sivaraman, J. / Li, Y. / Larocque, R. / Barbosa, J.A.R.G. / Smith, C. / Matte, A. / Schrag, J.D. / Cygler, M.
History
DepositionJul 17, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-AMINO-3-KETOBUTYRATE CONENZYME A LIGASE
B: 2-AMINO-3-KETOBUTYRATE CONENZYME A LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,7546
Polymers88,0262
Non-polymers7284
Water19,8711103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11780 Å2
ΔGint-47 kcal/mol
Surface area25700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.936, 98.659, 118.699
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailskbl forms a homodimer in solution as well as in the crystal. The monomers are related by a noncrystallographic twofold

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Components

#1: Protein 2-AMINO-3-KETOBUTYRATE CONENZYME A LIGASE


Mass: 44013.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
References: UniProt: P07912, UniProt: P0AB77*PLUS, glycine C-acetyltransferase
#2: Chemical ChemComp-AKB / 2-AMINO-3-KETOBUTYRIC ACID


Mass: 117.103 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H7NO3
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1103 / 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: 2.13 Å3/Da / Density % sol: 42.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: ammonium sulfate, glycerol, Na/K phosphate, DTT, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 18K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlprotein1drop
220 mMTris-HCl1drop
30.2 M1dropNaCl
41 mMEDTA1drop
52.2 Mammonium sulfate1reservoir
63.4 %(w/v)glycerol1reservoir
70.1 Msodium/potassium phosphate1reservoir
83 mMdithiothreitol1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONNSLS X8C10.979305
SYNCHROTRONNSLS X8C20.97955
SYNCHROTRONNSLS X8C30.961123
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDMay 28, 2000
ADSC QUANTUM 42CCDMay 28, 2000
ADSC QUANTUM 43CCDMay 28, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9793051
20.979551
30.9611231
ReflectionResolution: 2→100 Å / Num. all: 97661 / Num. obs: 97661 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 16.9

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Processing

Software
NameVersionClassification
SOLVEphasing
DMmodel building
ARP/wARP5model building
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
RefinementResolution: 2→12 Å / σ(F): -3 / σ(I): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.212 5094 -arbitrary, 10%
Rwork0.151 ---
all-50708 --
obs-50708 100 %-
Refinement stepCycle: LAST / Resolution: 2→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6089 0 46 1103 7238

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