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- PDB-6ezl: Crystal structure of aspartate aminotransferase from Trypanosoma ... -

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Basic information

Entry
Database: PDB / ID: 6ezl
TitleCrystal structure of aspartate aminotransferase from Trypanosoma cruzi at 2.07 Angstrom resolution
ComponentsAspartate aminotransferase
KeywordsTRANSFERASE / transaminase enzyme Trypanosomes metabolism
Function / homology
Function and homology information


aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / amino acid metabolic process / biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
Aspartate/other aminotransferase / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / 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 ...Aspartate/other aminotransferase / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Aspartate aminotransferase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsJagoe, W.N. / Khan, A.R.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation Ireland12/1A/1239 Ireland
CitationJournal: To Be Published
Title: Structure of aspartate aminotransferase from Trypanosoma Cruzi at 2.07 Angstrom resolution
Authors: Jagoe, W.N. / Barry, P.J.G. / Nolan, D.P. / Khan, A.R.
History
DepositionNov 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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

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Assembly

Deposited unit
A: Aspartate aminotransferase
B: Aspartate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,2414
Polymers89,7472
Non-polymers4942
Water9,098505
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-26 kcal/mol
Surface area29210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.495, 59.086, 139.015
Angle α, β, γ (deg.)90.00, 112.64, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Aspartate aminotransferase


Mass: 44873.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: pyridoxal phosphate at K252
Source: (gene. exp.) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / Gene: Tc00.1047053503841.70 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4D080, aspartate transaminase
#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.: 505 / 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: 2.49 Å3/Da / Density % sol: 50.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 0% PEG 6000 5% Glycerol 50mM Sodium Acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.07→45.38 Å / Num. obs: 54095 / % possible obs: 99.6 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 7.3
Reflection shellResolution: 2.07→2.13 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.864 / Mean I/σ(I) obs: 1.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4H51

4h51


Resolution: 2.07→45.376 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0.59 / Phase error: 23.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2293 1986 3.67 %
Rwork0.1796 --
obs0.1814 54047 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.07→45.376 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6102 0 30 505 6637
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126264
X-RAY DIFFRACTIONf_angle_d1.238503
X-RAY DIFFRACTIONf_dihedral_angle_d14.2393789
X-RAY DIFFRACTIONf_chiral_restr0.057943
X-RAY DIFFRACTIONf_plane_restr0.0081098
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.12180.31471330.27533710X-RAY DIFFRACTION100
2.1218-2.17920.33351440.24273705X-RAY DIFFRACTION100
2.1792-2.24330.26791470.21373673X-RAY DIFFRACTION100
2.2433-2.31570.241380.20993749X-RAY DIFFRACTION100
2.3157-2.39840.27611430.23711X-RAY DIFFRACTION100
2.3984-2.49450.25111430.1963682X-RAY DIFFRACTION100
2.4945-2.6080.24891410.19573724X-RAY DIFFRACTION100
2.608-2.74550.2551410.18423762X-RAY DIFFRACTION100
2.7455-2.91740.24361390.18513688X-RAY DIFFRACTION100
2.9174-3.14270.23051480.18433748X-RAY DIFFRACTION99
3.1427-3.45880.24061410.17693716X-RAY DIFFRACTION99
3.4588-3.95910.21911400.15393703X-RAY DIFFRACTION99
3.9591-4.9870.15851470.13513710X-RAY DIFFRACTION98
4.987-45.38660.20911410.17163780X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -13.5534 Å / Origin y: 38.8555 Å / Origin z: 29.7717 Å
111213212223313233
T0.1397 Å2-0.0256 Å20.0336 Å2-0.1177 Å20.0048 Å2--0.1387 Å2
L0.6906 °20.285 °20.6487 °2-0.2971 °20.3186 °2--1.0669 °2
S-0.0175 Å °-0.0472 Å °0.0591 Å °0.0183 Å °-0.0136 Å °0.0056 Å °-0.127 Å °-0.0151 Å °0.0254 Å °
Refinement TLS groupSelection details: all

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