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- PDB-2r5c: Aedes Kynurenine Aminotransferase in Complex with Cysteine -

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Basic information

Entry
Database: PDB / ID: 2r5c
TitleAedes Kynurenine Aminotransferase in Complex with Cysteine
Components(Kynurenine aminotransferase) x 2
KeywordsTRANSFERASE / Alpha and Beta protein / Pyridoxal-5-phosphate dependent transferase / Aminotransferase
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
Chem-C6P / Kynurenine aminotransferase / Kynurenine aminotransferase
Similarity search - Component
Biological speciesAedes aegypti (yellow fever mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsHan, Q. / Gao, Y.G. / Robinson, H. / Li, J.
CitationJournal: Biochemistry / Year: 2008
Title: Structural insight into the mechanism of substrate specificity of aedes kynurenine aminotransferase.
Authors: Han, Q. / Gao, Y.G. / Robinson, H. / Li, J.
History
DepositionSep 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 15, 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: Kynurenine aminotransferase
B: Kynurenine aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,2533
Polymers96,9002
Non-polymers3521
Water8,431468
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6490 Å2
ΔGint-32.2 kcal/mol
Surface area29360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.050, 95.678, 166.752
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


Mass: 48564.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: LLP at position 255 / Source: (gene. exp.) Aedes aegypti (yellow fever mosquito) / Strain: Liverpool / Gene: KAT / Plasmid: PBLUEBAC4.5 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9
References: UniProt: Q95VY4, UniProt: Q17CS8*PLUS, kynurenine-oxoglutarate transaminase, glutamine-phenylpyruvate transaminase
#2: Protein Kynurenine aminotransferase


Mass: 48336.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: LYS at position 255 / Source: (gene. exp.) Aedes aegypti (yellow fever mosquito) / Strain: Liverpool / Gene: KAT / Plasmid: PBLUEBAC4.5 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9
References: UniProt: Q95VY4, UniProt: Q17CS8*PLUS, kynurenine-oxoglutarate transaminase, glutamine-phenylpyruvate transaminase
#3: Chemical ChemComp-C6P / N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-L-CYSTEINE / 4-((1-CARBOXY-2-THIOL-ETHYLAMINO)-METHYL)-3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDINIUM


Mass: 352.301 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17N2O7PS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / 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: 2.31 Å3/Da / Density % sol: 46.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2 M ammonium sulfate, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 30, 2005 / Details: mirrors
RadiationMonochromator: Si (111) or (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.96→30 Å / Num. obs: 65484 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.072
Reflection shellResolution: 1.96→2.03 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.274 / % possible all: 67

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1yiy

1yiy


Resolution: 1.96→28.67 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.929 / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26708 3057 5.1 %RANDOM
Rwork0.21995 ---
obs0.2223 56757 91.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.546 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.96→28.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6661 0 22 468 7151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0226860
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8521.9639317
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.4055836
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.03524.539304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.458151152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1571528
X-RAY DIFFRACTIONr_chiral_restr0.3470.21003
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025225
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.230.23518
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3210.24618
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2449
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1180.225
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0970.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7421.54369
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.20126769
X-RAY DIFFRACTIONr_scbond_it3.89633012
X-RAY DIFFRACTIONr_scangle_it5.1384.52548
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.959→2.009 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 165 -
Rwork0.367 2817 -
obs--62.87 %

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