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- PDB-3e2z: Crystal structure of mouse kynurenine aminotransferase III in com... -

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Basic information

Entry
Database: PDB / ID: 3e2z
TitleCrystal structure of mouse kynurenine aminotransferase III in complex with kynurenine
Components(Kynurenine-oxoglutarate transaminase ...) x 2
KeywordsTRANSFERASE / LYASE / alpha beta protein / PLP dependent protein / Aminotransferase / Pyridoxal phosphate
Function / homology
Function and homology information


L-kynurenine catabolic process / kynurenine-glyoxylate transaminase / kynurenine-glyoxylate transaminase activity / cysteine-S-conjugate beta-lyase / cysteine-S-conjugate beta-lyase activity / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity / kynurenine metabolic process / 2-oxoglutarate metabolic process / amino acid metabolic process ...L-kynurenine catabolic process / kynurenine-glyoxylate transaminase / kynurenine-glyoxylate transaminase activity / cysteine-S-conjugate beta-lyase / cysteine-S-conjugate beta-lyase activity / 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
(2S)-2-amino-4-(2-aminophenyl)-4-oxobutanoic acid / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / Kynurenine--oxoglutarate transaminase 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsHan, Q. / Robinson, R. / Cai, T. / Tagle, D.A. / Li, J.
Citation
Journal: Mol. Cell. Biol. / Year: 2018
Title: Correction for Han et al., "Biochemical and Structural Properties of Mouse Kynurenine Aminotransferase III".
Authors: Han, Q. / Robinson, H. / Cai, T. / Tagle, D.A. / Li, J.
#1: Journal: Mol.Cell.Biol. / Year: 2009
Title: Biochemical and structural properties of mouse kynurenine aminotransferase III.
Authors: Han, Q. / Robinson, H. / Cai, T. / Tagle, D.A. / Li, J.
History
DepositionAug 6, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 1, 2018Group: Advisory / Data collection / Database references / Category: citation / citation_author / database_PDB_caveat / Item: _database_PDB_caveat.text
Revision 1.3Aug 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 1.4Nov 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

Downloads & links

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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)93,7119
Polymers92,6782
Non-polymers1,0337
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-30.4 kcal/mol
Surface area29380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.490, 91.490, 233.501
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Kynurenine-oxoglutarate transaminase ... , 2 types, 2 molecules AB

#1: Protein Kynurenine-oxoglutarate transaminase 3 / Kynurenine-oxoglutarate transaminase III / Kynurenine aminotransferase III / KATIII / Cysteine-S- ...Kynurenine-oxoglutarate transaminase III / Kynurenine aminotransferase III / KATIII / Cysteine-S-conjugate beta-lyase 2


Mass: 46453.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ccbl2, Kat3 / Plasmid: pBlueBac4.5 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q71RI9, kynurenine-oxoglutarate transaminase, cysteine-S-conjugate beta-lyase
#2: Protein Kynurenine-oxoglutarate transaminase 3 / Kynurenine-oxoglutarate transaminase III / Kynurenine aminotransferase III / KATIII / Cysteine-S- ...Kynurenine-oxoglutarate transaminase III / Kynurenine aminotransferase III / KATIII / Cysteine-S-conjugate beta-lyase 2


Mass: 46224.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ccbl2, Kat3 / Plasmid: pBlueBac4.5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q71RI9

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Non-polymers , 4 types, 90 molecules

#3: Chemical ChemComp-KYN / (2S)-2-amino-4-(2-aminophenyl)-4-oxobutanoic acid / L-KYNURENINE


Type: L-peptide linking / Mass: 208.214 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N2O3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13N2O5P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 21% PEG 400, 150 mM CaCl2, 10% Glycerol, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 27, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 25229 / Num. obs: 24119 / % possible obs: 95.6 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.12
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.39

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
DENZOdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2ZJG

2zjg


Resolution: 2.81→29.64 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.894 / Cross valid method: THROUGHOUT / ESU R Free: 0.371 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23654 1227 5.1 %RANDOM
Rwork0.19172 ---
obs0.19394 22779 95.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.643 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.81→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6521 0 70 83 6674
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0226764
X-RAY DIFFRACTIONr_angle_refined_deg2.2051.9699185
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.8975818
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.91924.225284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.06151136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9921528
X-RAY DIFFRACTIONr_chiral_restr0.3570.21000
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025094
X-RAY DIFFRACTIONr_nbd_refined0.2790.23330
X-RAY DIFFRACTIONr_nbtor_refined0.3390.24617
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2316
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.22
X-RAY DIFFRACTIONr_mcbond_it1.0361.54110
X-RAY DIFFRACTIONr_mcangle_it1.90326676
X-RAY DIFFRACTIONr_scbond_it2.9732654
X-RAY DIFFRACTIONr_scangle_it4.5144.52509
LS refinement shellResolution: 2.81→2.88 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 71 -
Rwork0.262 1085 -
obs--64.12 %

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