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- PDB-3fvu: Crystal Structure of Human Kynurenine Aminotransferase I in Compl... -

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Basic information

Entry
Database: PDB / ID: 3fvu
TitleCrystal Structure of Human Kynurenine Aminotransferase I in Complex with Indole-3-acetic Acid
ComponentsKynurenine--oxoglutarate transaminase 1
KeywordsLyase / Transferase / alpha beta protein / PLP dependent protein / aminotransferase / pyridoxal phosphate
Function / homology
Function and homology information


glutamine-phenylpyruvate transaminase / glutamine-phenylpyruvate transaminase activity / L-kynurenine catabolic process / cysteine-S-conjugate beta-lyase / cysteine-S-conjugate beta-lyase activity / Phenylalanine metabolism / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity / kynurenine metabolic process / Glutamate and glutamine metabolism ...glutamine-phenylpyruvate transaminase / glutamine-phenylpyruvate transaminase activity / L-kynurenine catabolic process / cysteine-S-conjugate beta-lyase / cysteine-S-conjugate beta-lyase activity / Phenylalanine metabolism / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity / kynurenine metabolic process / Glutamate and glutamine metabolism / Tryptophan catabolism / biosynthetic process / response to bacterium / pyridoxal phosphate binding / protein homodimerization activity / mitochondrion / cytosol / 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
1H-INDOL-3-YLACETIC ACID / Kynurenine--oxoglutarate transaminase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsHan, Q. / Robinson, H. / Cai, T. / Tagle, D.A. / Li, J.
CitationJournal: J.Med.Chem. / Year: 2009
Title: Structural insight into the inhibition of human kynurenine aminotransferase I/glutamine transaminase K
Authors: Han, Q. / Robinson, H. / Cai, T. / Tagle, D.A. / Li, J.
History
DepositionJan 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Sep 6, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 22, 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 1
B: Kynurenine--oxoglutarate transaminase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,16911
Polymers96,3122
Non-polymers8579
Water10,629590
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8590 Å2
ΔGint-38 kcal/mol
Surface area29920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.364, 108.454, 81.867
Angle α, β, γ (deg.)90.00, 114.20, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Kynurenine--oxoglutarate transaminase 1 / Kynurenine--oxoglutarate transaminase I / Kynurenine aminotransferase I / KATI / Glutamine-- ...Kynurenine--oxoglutarate transaminase I / Kynurenine aminotransferase I / KATI / Glutamine--phenylpyruvate transaminase / Glutamine transaminase K / GTK / Cysteine-S-conjugate beta-lyase


Mass: 48156.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCBL1 / Plasmid: pBlueBac4.5 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q16773, kynurenine-oxoglutarate transaminase, glutamine-phenylpyruvate transaminase, cysteine-S-conjugate beta-lyase
#2: Chemical ChemComp-IAC / 1H-INDOL-3-YLACETIC ACID / INDOLE ACETIC ACID


Mass: 175.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H9NO2 / Comment: hormone*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 590 / 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: 2.24 Å3/Da / Density % sol: 44.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 22% PEG 400, sodium acetate 0.2 M, Tris 0.1 M, 4% glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: 1.55→30 Å / Num. obs: 122095 / Redundancy: 7.3 % / Rmerge(I) obs: 0.049
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3.8

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Processing

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

1w7l


Resolution: 1.55→29.22 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.955 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21014 6120 5 %RANDOM
Rwork0.18451 ---
obs0.18581 115737 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.974 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20.01 Å2
2--0.03 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.55→29.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6738 0 58 590 7386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226987
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.331.9619481
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3985836
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.73723.988326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.887151138
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4071536
X-RAY DIFFRACTIONr_chiral_restr0.0920.21000
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025372
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.23492
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.24839
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2552
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1490.25
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6971.54194
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.25926804
X-RAY DIFFRACTIONr_scbond_it1.96732793
X-RAY DIFFRACTIONr_scangle_it3.0974.52677
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.551→1.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 435 -
Rwork0.266 8363 -
obs--99 %

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