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- PDB-1yiy: Aedes aegypti kynurenine aminotransferase -

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Basic information

Entry
Database: PDB / ID: 1yiy
TitleAedes aegypti kynurenine aminotransferase
Componentskynurenine aminotransferase; glutamine transaminase K
KeywordsTRANSFERASE / kynurenine / kynurenic acid / kynurenine aminotrasferase / Aedes / mosquito / PLP-enzyme / PMP / pyridoxamine phosphate
Function / homology
Function and homology information


L-kynurenine catabolic process / kynurenine-glyoxylate transaminase / kynurenine-glyoxylate transaminase activity / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity / Transferases; Transferring nitrogenous groups; Transaminases / biosynthetic process / pyridoxal phosphate binding / mitochondrion
Similarity search - Function
: / 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 ...: / 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
BROMIDE ION / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / Kynurenine aminotransferase / Kynurenine aminotransferase
Similarity search - Component
Biological speciesAedes aegypti (yellow fever mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHan, Q. / Gao, Y.G. / Robinson, H. / Ding, H. / Wilson, S. / Li, J.
CitationJournal: FEBS J. / Year: 2005
Title: Crystal structures of Aedes aegypti kynurenine aminotransferase.
Authors: Han, Q. / Gao, Y.G. / Robinson, H. / Ding, H. / Wilson, S. / Li, J.
History
DepositionJan 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: kynurenine aminotransferase; glutamine transaminase K
B: kynurenine aminotransferase; glutamine transaminase K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,5689
Polymers96,6722
Non-polymers8967
Water7,927440
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7880 Å2
ΔGint-38 kcal/mol
Surface area29400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.358, 95.316, 167.674
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein kynurenine aminotransferase; glutamine transaminase K


Mass: 48336.137 Da / Num. of mol.: 2 / Fragment: kynurenine aminotransferase (Residues 49-477)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aedes aegypti (yellow fever mosquito) / Gene: KAT / Plasmid: PBLUE BAC4.5-BAC-N-BLUE / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9
References: UniProt: Q95VY4, UniProt: Q17CS8*PLUS, kynurenine-oxoglutarate transaminase, glutamine-phenylpyruvate transaminase
#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13N2O5P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / 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: 2.29 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 1000, TRIS.HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.97 Å
DetectorType: SIEMENS FOUR-CIRCLE / Detector: DIFFRACTOMETER / Date: Aug 28, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.9→10 Å / Num. all: 68715 / Num. obs: 68715 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Rmerge(I) obs: 0.063
Reflection shellResolution: 1.9→1.97 Å / % possible all: 90.5

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1gck, 1v2d

1gck

1v2d


Resolution: 1.9→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 4 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rwork0.218 ---
Rfree-3153 -RANDOM
all-66171 --
obs-66171 97.1 %-
Displacement parametersBiso mean: 20.48 Å2
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6630 0 37 440 7107
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.007
X-RAY DIFFRACTIONs_bond_d1.72

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