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- PDB-3tqx: Structure of the 2-amino-3-ketobutyrate coenzyme A ligase (kbl) f... -

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Basic information

Entry
Database: PDB / ID: 3tqx
TitleStructure of the 2-amino-3-ketobutyrate coenzyme A ligase (kbl) from Coxiella burnetii
Components2-amino-3-ketobutyrate coenzyme A ligase
KeywordsTRANSFERASE / Energy metabolism
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 / 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) ...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
PYRIDOXAL-5'-PHOSPHATE / 2-amino-3-ketobutyrate coenzyme A ligase
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.304 Å
AuthorsCheung, J. / Franklin, M.C. / Rudolph, M. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J.
CitationJournal: Proteins / Year: 2015
Title: Structural genomics for drug design against the pathogen Coxiella burnetii.
Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.
History
DepositionSep 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Jan 27, 2016Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)88,7464
Polymers88,2522
Non-polymers4942
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9880 Å2
ΔGint-61 kcal/mol
Surface area29080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.820, 114.850, 136.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein 2-amino-3-ketobutyrate coenzyme A ligase


Mass: 44125.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxiella burnetii (bacteria) / Strain: RSA493 / Gene: CBU_0111, kbl / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83F40, glycine C-acetyltransferase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


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


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.53 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1M MES pH 5.0, 20% PEG6000, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 29, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twinOperator: -k,-h,-l / Fraction: 0.308
ReflectionResolution: 2.3→30 Å / Num. all: 39662 / Num. obs: 38908 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.106 / Χ2: 1.24 / Net I/σ(I): 6.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.3430.42518310.76195.2
2.34-2.383.10.40918740.763194.8
2.38-2.433.20.41419330.724197.4
2.43-2.483.30.39518860.79197.1
2.48-2.533.40.3618720.81195.7
2.53-2.593.50.32118940.862196.4
2.59-2.653.50.30819180.84197.9
2.65-2.733.60.26719140.945197.4
2.73-2.813.60.25319090.931197.9
2.81-2.93.60.20819341.014197.6
2.9-33.70.17819521.027198.6
3-3.123.70.14419361.084199
3.12-3.263.70.12719631.231199.1
3.26-3.433.80.10119681.293199.3
3.43-3.653.90.0919951.507199.8
3.65-3.934.10.07819711.535199.9
3.93-4.334.10.0720001.654199.9
4.33-4.954.10.06120101.605199.9
4.95-6.2340.06920321.5751100
6.23-303.80.05621162.772199.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FC4

1fc4


Resolution: 2.304→29.368 Å / Occupancy max: 1 / Occupancy min: 0.39 / FOM work R set: 0.7398 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 32.28 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2671 1885 5.17 %random
Rwork0.2152 ---
all0.218 41902 --
obs0.2184 36426 91.43 %-
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.907 Å2 / ksol: 0.366 e/Å3
Displacement parametersBiso max: 107.36 Å2 / Biso mean: 33.4426 Å2 / Biso min: 10.94 Å2
Baniso -1Baniso -2Baniso -3
1-4.0477 Å20 Å2-0 Å2
2--2.5883 Å2-0 Å2
3----6.6359 Å2
Refinement stepCycle: LAST / Resolution: 2.304→29.368 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6086 0 32 239 6357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026214
X-RAY DIFFRACTIONf_angle_d0.6068382
X-RAY DIFFRACTIONf_chiral_restr0.043940
X-RAY DIFFRACTIONf_plane_restr0.0021090
X-RAY DIFFRACTIONf_dihedral_angle_d12.8722330
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3103-2.37150.33511580.25092184234274
2.3715-2.43970.35581000.25852361246180
2.4397-2.51650.32131550.25562342249779
2.5165-2.60390.31031010.25962436253782
2.6039-2.7050.29651400.24832452259283
2.705-2.82390.36511180.26142524264286
2.8239-2.96680.33111210.24952592271387
2.9668-3.14390.30381560.24372653280990
3.1439-3.37270.32251030.22282796289993
3.3727-3.68710.24851820.2092756293893
3.6871-4.16540.2654940.18962890298497
4.1654-5.05940.24061960.16842823301993
5.0594-8.53710.2071890.19692891308094

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