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- PDB-2zjg: Crystal structural of mouse kynurenine aminotransferase III -

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Basic information

Entry
Database: PDB / ID: 2zjg
TitleCrystal structural of mouse kynurenine aminotransferase III
ComponentsKynurenine-oxoglutarate transaminase 3
KeywordsTRANSFERASE / alpha beta protein / PLP dependent protein / Aminotransferase / Lyase / Pyridoxal phosphate
Function / homology
Function and homology information


cysteine-S-conjugate beta-lyase activity / L-kynurenine catabolic process / kynurenine-glyoxylate transaminase activity / kynurenine-glyoxylate transaminase / cysteine-S-conjugate beta-lyase / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity / kynurenine metabolic process / 2-oxoglutarate metabolic process / amino acid metabolic process ...cysteine-S-conjugate beta-lyase activity / L-kynurenine catabolic process / kynurenine-glyoxylate transaminase activity / kynurenine-glyoxylate transaminase / cysteine-S-conjugate beta-lyase / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity / kynurenine metabolic process / 2-oxoglutarate metabolic process / amino acid metabolic process / biosynthetic process / pyridoxal phosphate binding / protein homodimerization activity / mitochondrion / cytoplasm
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
Kynurenine--oxoglutarate transaminase 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsHan, Q. / Cai, T. / Tagle, D.A. / Robinson, H. / Li, J.
CitationJournal: To be Published
Title: Structural and functional characterization of mouse kynurenine aminotransferase III
Authors: Han, Q. / Cai, T. / Tagle, D.A. / Robinson, H. / Li, J.
History
DepositionMar 7, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 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-oxoglutarate transaminase 3
B: Kynurenine-oxoglutarate transaminase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,73511
Polymers92,9062
Non-polymers8299
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7760 Å2
ΔGint-26.1 kcal/mol
Surface area28640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.090, 91.090, 233.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Kynurenine-oxoglutarate transaminase 3 / Kynurenine-oxoglutarate transaminase III / Kynurenine aminotransferase III / KATIII / kynurenine ...Kynurenine-oxoglutarate transaminase III / Kynurenine aminotransferase III / KATIII / kynurenine glyoxylate aminotransferase / glutamine transaminase K


Mass: 46453.098 Da / Num. of mol.: 2 / Fragment: UNP residues 42-451
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ccbl2, Kat3 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q71RI9, kynurenine-oxoglutarate transaminase, kynurenine-glyoxylate transaminase, glutamine-phenylpyruvate transaminase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.6 Å3/Da / Density % sol: 52.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG2000, 150mM CaCl2, 5% glycerol, 200mM HEPES, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0908 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 21, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0908 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 20485 / % possible obs: 97.4 % / Redundancy: 12 % / Rmerge(I) obs: 0.15
Reflection shellResolution: 3→3.11 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.47 / % possible all: 81.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
DENZOdata reduction
SCALAdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W7L

1w7l


Resolution: 3→29.58 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.914 / Cross valid method: THROUGHOUT / ESU R Free: 0.427 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23258 999 5 %RANDOM
Rwork0.22163 ---
obs0.22217 18849 97.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.328 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 3→29.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6536 0 54 104 6694
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0226759
X-RAY DIFFRACTIONr_angle_refined_deg2.0491.9679171
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.4245818
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.86624.225284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.022151136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2951528
X-RAY DIFFRACTIONr_chiral_restr0.2850.2998
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025052
X-RAY DIFFRACTIONr_nbd_refined0.2840.23458
X-RAY DIFFRACTIONr_nbtor_refined0.350.24696
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.2333
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3010.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5160.22
X-RAY DIFFRACTIONr_mcbond_it1.0931.54100
X-RAY DIFFRACTIONr_mcangle_it1.99726662
X-RAY DIFFRACTIONr_scbond_it3.03732659
X-RAY DIFFRACTIONr_scangle_it4.5244.52509
LS refinement shellResolution: 3.003→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 58 -
Rwork0.317 1086 -
obs--79.01 %

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