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- PDB-1w7n: Crystal structure of human kynurenine aminotransferase I in PMP form -

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Basic information

Entry
Database: PDB / ID: 1w7n
TitleCrystal structure of human kynurenine aminotransferase I in PMP form
ComponentsKYNURENINE--OXOGLUTARATE TRANSAMINASE I
KeywordsTRANSFERASE / KYNURENINE PATHWAY / KYNURENIC ACID / PLP-ENZYME / AMINOTRANSFERASE / LYASE / MULTIFUNCTIONAL ENZYME / PYRIDOXAL PHOSPHATE
Function / homology
Function and homology information


glutamine-phenylpyruvate transaminase / glutamine-phenylpyruvate transaminase activity / L-kynurenine catabolic process / cysteine-S-conjugate beta-lyase activity / cysteine-S-conjugate beta-lyase / 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 activity / cysteine-S-conjugate beta-lyase / 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
4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / Kynurenine--oxoglutarate transaminase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsRossi, F. / Han, Q. / Li, J. / Li, J. / Rizzi, M.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystal Structure of Human Kynurenine Aminotransferase I
Authors: Rossi, F. / Han, Q. / Li, J. / Li, J. / Rizzi, M.
History
DepositionSep 6, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 8, 2004Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Source and taxonomy / Version format compliance
Revision 1.2Dec 13, 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--OXOGLUTARATE TRANSAMINASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1762
Polymers47,9281
Non-polymers2481
Water3,549197
1
A: KYNURENINE--OXOGLUTARATE TRANSAMINASE I
hetero molecules

A: KYNURENINE--OXOGLUTARATE TRANSAMINASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,3524
Polymers95,8562
Non-polymers4962
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
Buried area6960 Å2
ΔGint-32.5 kcal/mol
Surface area30100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.461, 145.461, 67.087
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-2060-

HOH

21A-2066-

HOH

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Components

#1: Protein KYNURENINE--OXOGLUTARATE TRANSAMINASE I / KYNURENINE AMINOTRANSFERASE I / KATI / GLUTAMINE-PHENYLPYRUVATE TRANSAMINASE / GLUTAMINE ...KYNURENINE AMINOTRANSFERASE I / KATI / GLUTAMINE-PHENYLPYRUVATE TRANSAMINASE / GLUTAMINE TRANSAMINASE K / GTK / CYSTEINE-S-CONJUGATE BETA-LYASE


Mass: 47927.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Organ: LIVER / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: Q16773, cysteine-S-conjugate beta-lyase
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYTIC ACTIVITY: L-KYNURENINE + 2-OXOGLUTARATE = 4-(2- AMINOPHENYL)-2,4-DIOXOBUTANOATE + L-GLUTAMATE.

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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: 4.27 Å3/Da / Density % sol: 71.23 %
Crystal growpH: 7 / Details: pH 7.00
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
24.5 Mammonium formate1reservoir
30.1 MTris1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: MSC / Detector: AREA DETECTOR / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 18243 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.1
Reflection
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 30 Å / Num. measured all: 110645 / Rmerge(I) obs: 0.096

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W7L

1w7l


Resolution: 2.9→38.92 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.917 / SU B: 11.497 / SU ML: 0.217 / Cross valid method: THROUGHOUT / ESU R: 0.501 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22 564 3.1 %RANDOM
Rwork0.171 ---
obs0.172 17662 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 50.84 Å2
Baniso -1Baniso -2Baniso -3
1--4.15 Å2-2.07 Å20 Å2
2---4.15 Å20 Å2
3---6.22 Å2
Refinement stepCycle: LAST / Resolution: 2.9→38.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3321 0 16 197 3534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223432
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.661.9464658
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9755413
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1040.2494
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022646
X-RAY DIFFRACTIONr_gen_planes_other00.021
X-RAY DIFFRACTIONr_nbd_refined0.2410.21852
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2199
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.284
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8011.52072
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.57123358
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.23531360
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9234.51300
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.3 40
Rwork0.252 1288
Software
*PLUS
Version: 5.1.24 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.9 Å / Rfactor Rfree: 0.22 / Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.017
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.66

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