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- PDB-4wp0: Crystal structure of human kynurenine aminotransferase-I with a C... -

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Basic information

Entry
Database: PDB / ID: 4wp0
TitleCrystal structure of human kynurenine aminotransferase-I with a C-terminal V5-hexahistidine tag
ComponentsKynurenine--oxoglutarate transaminase 1
KeywordsLyase / Transferase / PLP dependent Pyridoxal phosphate Transaminase Aminotransferase cofactor Lysine modification Alpha beta protein
Function / homology
Function and homology information


glutamine-phenylpyruvate transaminase / glutamine-phenylpyruvate transaminase activity / cysteine-S-conjugate beta-lyase activity / L-kynurenine catabolic process / 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 / cysteine-S-conjugate beta-lyase activity / L-kynurenine catabolic process / 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 / cytoplasm / cytosol
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 / Alpha-Beta Complex ...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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
Model detailsThe protein was expressed with a C-terminal V5-hexahistidine epitope tag
AuthorsNadvi, N.A. / Salam, N.K. / Park, J. / Akladios, F.N. / Kapoor, V. / Collyer, C.A. / Gorrell, M.D. / Church, W.B.
CitationJournal: To be published
Title: Crystal structure of human kynurenine aminotransferase-I in a novel space group
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 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Non-polymer description
Revision 1.2Sep 27, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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

Downloads & links

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Assembly

Deposited unit
A: Kynurenine--oxoglutarate transaminase 1
B: Kynurenine--oxoglutarate transaminase 1
C: Kynurenine--oxoglutarate transaminase 1
D: Kynurenine--oxoglutarate transaminase 1


Theoretical massNumber of molelcules
Total (without water)215,2894
Polymers215,2894
Non-polymers00
Water2,072115
1
A: Kynurenine--oxoglutarate transaminase 1
B: Kynurenine--oxoglutarate transaminase 1


Theoretical massNumber of molelcules
Total (without water)107,6452
Polymers107,6452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-30 kcal/mol
Surface area30370 Å2
MethodPISA
2
C: Kynurenine--oxoglutarate transaminase 1
D: Kynurenine--oxoglutarate transaminase 1


Theoretical massNumber of molelcules
Total (without water)107,6452
Polymers107,6452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-29 kcal/mol
Surface area30360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)231.150, 231.150, 56.105
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
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: 53822.359 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCBL1 / Plasmid: pENTR/SD/D-TOPO
Details (production host): entry clone for baculodirect gateway system
Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q16773, kynurenine-oxoglutarate transaminase, cysteine-S-conjugate beta-lyase, glutamine-phenylpyruvate transaminase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.02 Å3/Da / Density % sol: 39.18 % / Mosaicity: 0.72 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3 / Details: 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: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 5, 2010
RadiationMonochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 33384 / % possible obs: 94.9 % / Redundancy: 4.7 % / Biso Wilson estimate: 55.51 Å2 / Rmerge(I) obs: 0.262 / Χ2: 1.159 / Net I/av σ(I): 3.907 / Net I/σ(I): 4.9 / Num. measured all: 155793
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allΧ2% possible allRmerge(I) obs
3-3.114.632771.4594
3.11-3.234.632621.30694.90.898
3.23-3.384.733381.1894.80.705
3.38-3.564.633031.06594.90.531
3.56-3.784.733411.18395.20.381
3.78-4.074.733461.013960.288
4.07-4.484.733691.09696.20.209
4.48-5.134.733470.99694.10.188
5.13-6.464.733541.232950.191
6.46-504.734471.08293.80.075

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.99 Å48.94 Å
Translation2.99 Å48.94 Å

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Processing

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

4wlh


Resolution: 3→48.941 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2665 1672 5.03 %
Rwork0.2344 31559 -
obs0.236 33231 93.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.39 Å2 / Biso mean: 53.4636 Å2 / Biso min: 36.2 Å2
Refinement stepCycle: final / Resolution: 3→48.941 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13368 0 0 115 13483
Biso mean---56.27 -
Num. residues----1660
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213752
X-RAY DIFFRACTIONf_angle_d0.74518668
X-RAY DIFFRACTIONf_chiral_restr0.0291985
X-RAY DIFFRACTIONf_plane_restr0.0032411
X-RAY DIFFRACTIONf_dihedral_angle_d13.8755012
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9854-3.07330.3911290.3672316244584
3.0733-3.17240.37161300.34822639276994
3.1724-3.28580.41411220.33142595271793
3.2858-3.41730.36111440.30882625276996
3.4173-3.57280.34441420.27652641278395
3.5728-3.76110.29791350.25252655279095
3.7611-3.99670.26041550.23982652280795
3.9967-4.30510.21161500.20362649279995
4.3051-4.7380.21141350.18662685282096
4.738-5.42280.24291570.19542658281595
5.4228-6.82920.2211410.21462679282094
6.8292-48.94720.21141320.17312765289794

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