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- PDB-4wlj: High resolution crystal structure of human kynurenine aminotransf... -

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Basic information

Entry
Database: PDB / ID: 4wlj
TitleHigh resolution crystal structure of human kynurenine aminotransferase-I in complex with aminooxyacetate
ComponentsKynurenine--oxoglutarate transaminase 1
KeywordsTRANSFERASE / Lysine modification / Transaminase / Aminotransferase / Alpha beta protein Ligand / AOAA / Deoxy Aminopyridoxal 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'-ACETYLYAMINO-PYRIDOXAL-5'-PHOSPHATE / Kynurenine--oxoglutarate transaminase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.54 Å
Model detailsThe inhibitor aminooxyacetate forms an oxime with cofactor PLP that displaces the Schiff-base ...The inhibitor aminooxyacetate forms an oxime with cofactor PLP that displaces the Schiff-base linkage with the catalytic lysine247
AuthorsNadvi, N.A. / Salam, N.K. / Park, J. / Akladios, F.N. / Kapoor, V. / Collyer, C.A. / Gorrell, M.D. / Church, W.B.
CitationJournal: Protein Sci. / Year: 2017
Title: High resolution crystal structures of human kynurenine aminotransferase-I bound to PLP cofactor, and in complex with aminooxyacetate.
Authors: Nadvi, N.A. / Salam, N.K. / Park, J. / Akladios, F.N. / Kapoor, V. / Collyer, C.A. / Gorrell, M.D. / Church, W.B.
History
DepositionOct 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references
Revision 1.2Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)96,5004
Polymers95,8562
Non-polymers6442
Water7,062392
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7380 Å2
ΔGint-36 kcal/mol
Surface area30750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.740, 107.650, 81.750
Angle α, β, γ (deg.)90.000, 112.980, 90.000
Int Tables number5
Space group name H-MC121
Detailsbiological unit is the same as asym.

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Components

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


Mass: 47927.879 Da / Num. of mol.: 2 / Fragment: unp residues 87-392
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, cysteine-S-conjugate beta-lyase, glutamine-phenylpyruvate transaminase
#2: Chemical ChemComp-IK2 / 4'-DEOXY-4'-ACETYLYAMINO-PYRIDOXAL-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N2O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 2.19 Å3/Da / Density % sol: 43.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 5 mM AOAA, 29% PEG 4000, 0.2 M sodium acetate, 0.1 M Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95369 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 2, 2011
RadiationMonochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 1.54→75.262 Å / Num. all: 108232 / Num. obs: 108232 / % possible obs: 89.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 14.48 Å2 / Rpim(I) all: 0.033 / Rrim(I) all: 0.086 / Rsym value: 0.079 / Net I/av σ(I): 7.198 / Net I/σ(I): 13.2 / Num. measured all: 683702
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.54-1.625.20.6671.284844164410.3140.6672.293.9
1.62-1.725.80.4861.692802160790.2160.4863.296.9
1.72-1.845.80.332.483284142780.1460.334.791.4
1.84-1.996.20.229366132107140.0980.2297.673.5
1.99-2.186.80.1275.981045120000.0530.12712.689.6
2.18-2.436.90.0997.272336105170.040.09915.786.7
2.43-2.817.30.06410.97065097000.0250.0642290.5
2.81-3.447.30.04514.26396087900.0180.04530.797.1
3.44-4.877.20.0415.34188658250.0160.0441.682.8
4.87-26.946.90.04311.72676338880.0180.04339.399.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
Blu-Icedata collection
PHASER2.2.1phasing
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WLH

4wlh


Resolution: 1.54→26.94 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.47 / Stereochemistry target values: ML
Details: The high resolution at which this structure was determined allowed the identification of residues with alternate conformations. Four regions in each chain were observed to be highly ...Details: The high resolution at which this structure was determined allowed the identification of residues with alternate conformations. Four regions in each chain were observed to be highly disordered with generally poorer election density: residues 15-29, 147-154, 355-359 and the C-terminus (419-422). Residues 147-154 were removed from the final model due to the absence of unambiguous election density. For residues in the other disordered regions electron density could be observed for most of the main chain atoms, but was less unambiguous for the side-chains. These residues are in the final model, with both the occupancy and temperature factors set to zero for most of these residues, due to the existence of a level of evidence for their location.
RfactorNum. reflection% reflection
Rfree0.2274 5348 4.98 %
Rwork0.1974 102037 -
obs0.1989 107385 89.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.64 Å2 / Biso mean: 18.5506 Å2 / Biso min: 7.07 Å2
Refinement stepCycle: final / Resolution: 1.54→26.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6618 0 66 392 7076
Biso mean--18.44 21.26 -
Num. residues----782
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116872
X-RAY DIFFRACTIONf_angle_d1.3619330
X-RAY DIFFRACTIONf_chiral_restr0.056990
X-RAY DIFFRACTIONf_plane_restr0.0081204
X-RAY DIFFRACTIONf_dihedral_angle_d13.7542524
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.54-1.55750.29652060.24763332353889
1.5575-1.57580.26081790.23123495367491
1.5758-1.5950.27981940.22753585377996
1.595-1.61520.27242070.21563745395297
1.6152-1.63650.22351920.20983716390898
1.6365-1.65890.25081870.19543781396898
1.6589-1.68260.22061830.19353710389398
1.6826-1.70770.24911980.18853762396099
1.7077-1.73440.2381140.18652349246361
1.7344-1.76280.27472150.18833746396199
1.7628-1.79320.241920.19373795398799
1.7932-1.82580.2591910.185338274018100
1.8258-1.86090.25841930.2033816400999
1.8609-1.89890.39951250.33062600272568
1.8989-1.94020.43391370.38282780291773
1.9402-1.98530.3321010.23822033213498
1.9853-2.03490.23142140.190337964010100
2.0349-2.08990.23571420.197324962638100
2.0899-2.15140.2321910.197838524043100
2.1514-2.22080.22981770.24063572374994
2.2208-2.30010.32941370.28992121225856
2.3001-2.39220.21091950.17993793398899
2.3922-2.5010.20082080.175237893997100
2.501-2.63270.19861810.180538474028100
2.6327-2.79750.2161450.18622842298775
2.7975-3.01320.21731990.190838384037100
3.0132-3.3160.21831930.192238384031100
3.316-3.79470.2281500.18372881303175
3.7947-4.77650.15171890.15083399358888
4.7765-26.94420.18262130.173239014114100

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