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- PDB-6d0a: Crystal structure of Kynurenine Aminotransferase-II in apo-form, ... -

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Basic information

Entry
Database: PDB / ID: 6d0a
TitleCrystal structure of Kynurenine Aminotransferase-II in apo-form, at 1.47 A resolution
ComponentsKynurenine/alpha-aminoadipate aminotransferase, mitochondrial
KeywordsTRANSFERASE / PLP-dependent / hexahistidine tag / alpha-beta fold
Function / homology
Function and homology information


glycine transaminase / methionine-glyoxylate transaminase / glycine:2-oxoglutarate aminotransferase activity / methionine-glyoxylate transaminase activity / 2-aminoadipate transaminase / alpha-amino acid metabolic process / 2-aminoadipate transaminase activity / kynurenine-glyoxylate transaminase / kynurenine-glyoxylate transaminase activity / L-lysine catabolic process to acetyl-CoA via saccharopine ...glycine transaminase / methionine-glyoxylate transaminase / glycine:2-oxoglutarate aminotransferase activity / methionine-glyoxylate transaminase activity / 2-aminoadipate transaminase / alpha-amino acid metabolic process / 2-aminoadipate transaminase activity / kynurenine-glyoxylate transaminase / kynurenine-glyoxylate transaminase activity / L-lysine catabolic process to acetyl-CoA via saccharopine / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity / kynurenine metabolic process / Lysine catabolism / glutamate metabolic process / 2-oxoglutarate metabolic process / Tryptophan catabolism / biosynthetic process / pyridoxal phosphate binding / mitochondrial matrix / protein homodimerization activity
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, 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, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46809418277 Å
AuthorsJayawickrama, G.S. / Sun, G. / Nematollahi, A. / Church, W.B.
CitationJournal: To Be Published
Title: Crystal structure of Kynurenine Aminotransferase-II in apo-form
Authors: Jayawickrama, G.S. / Sun, G. / Nematollahi, A. / Church, W.B.
History
DepositionApr 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / 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

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Assembly

Deposited unit
A: Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)48,2291
Polymers48,2291
Non-polymers00
Water8,701483
1
A: Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial

A: Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)96,4592
Polymers96,4592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7830 Å2
ΔGint-56 kcal/mol
Surface area32020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.765, 102.765, 86.498
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Components on special symmetry positions
IDModelComponents
11A-566-

HOH

21A-767-

HOH

31A-796-

HOH

41A-873-

HOH

51A-979-

HOH

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Components

#1: Protein Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial / KAT/AadAT / 2-aminoadipate aminotransferase / 2-aminoadipate transaminase / Alpha-aminoadipate ...KAT/AadAT / 2-aminoadipate aminotransferase / 2-aminoadipate transaminase / Alpha-aminoadipate aminotransferase / AadAT / Kynurenine aminotransferase II / Kynurenine--oxoglutarate aminotransferase II / Kynurenine--oxoglutarate transaminase 2 / Kynurenine--oxoglutarate transaminase II


Mass: 48229.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: There is a hexahistidine tag on the N-terminal end.
Source: (gene. exp.) Homo sapiens (human) / Gene: AADAT, KAT2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8N5Z0, 2-aminoadipate transaminase, kynurenine-oxoglutarate transaminase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 483 / 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: 2.37 Å3/Da / Density % sol: 48.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Protein 10 mg/mL was mixed with an equal volume of a reservoir solution containing 200 mM NaCl, 0.1 M NaCitrate pH 5.6, 24% PEG4K and equilibrated against 1 mL of a reservoir solution.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.468→45.958 Å / Num. obs: 79172 / % possible obs: 99.89 % / Redundancy: 2 % / Biso Wilson estimate: 14.4876525592 Å2 / Rmerge(I) obs: 0.05847 / Rpim(I) all: 0.01158 / Rrim(I) all: 0.05963 / Net I/σ(I): 41.07
Reflection shellResolution: 1.468→1.521 Å / Rmerge(I) obs: 0.2693 / Mean I/σ(I) obs: 11.61 / Num. unique obs: 7700 / Rpim(I) all: 0.05284 / Rrim(I) all: 0.2746 / % possible all: 98.97

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Processing

Software
NameVersionClassification
phenix.refine1.12_2829refinement
PHENIX1.12_2829refinement
XDSdata reduction
Aimlessdata scaling
PHENIX(1.12-2829:2017)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EUN

5eun


Resolution: 1.46809418277→45.9579051416 Å / SU ML: 0.10695018247 / Cross valid method: FREE R-VALUE / σ(F): 1.38369573649 / Phase error: 17.2883698255
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.187901673544 2000 2.52624133183 %
Rwork0.173515953791 77169 -
obs0.173889680561 79169 99.8914894959 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.030880913 Å2
Refinement stepCycle: LAST / Resolution: 1.46809418277→45.9579051416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3392 0 0 483 3875
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008691714087153480
X-RAY DIFFRACTIONf_angle_d0.9988250401114724
X-RAY DIFFRACTIONf_chiral_restr0.0762402474895521
X-RAY DIFFRACTIONf_plane_restr0.00788802967208611
X-RAY DIFFRACTIONf_dihedral_angle_d11.60478004691298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4681-1.50480.1988184626881380.18477428425309X-RAY DIFFRACTION98.5525601592
1.5048-1.54550.1912475689791420.1771922552525476X-RAY DIFFRACTION100
1.5455-1.5910.1802388408731400.1730743526285428X-RAY DIFFRACTION99.9820434548
1.591-1.64230.195801799451420.1758048297615473X-RAY DIFFRACTION100
1.6423-1.7010.1894456252021420.173777580095463X-RAY DIFFRACTION100
1.701-1.76910.1883912090461410.1757641530315470X-RAY DIFFRACTION100
1.7691-1.84970.1735923167161410.1711168083835448X-RAY DIFFRACTION100
1.8497-1.94720.1907572218271430.1751874404545504X-RAY DIFFRACTION100
1.9472-2.06920.2148334800451420.1672228316455490X-RAY DIFFRACTION100
2.0692-2.22890.1835001608241440.1655055071365509X-RAY DIFFRACTION100
2.2289-2.45320.1762108807841430.1670966911095545X-RAY DIFFRACTION100
2.4532-2.80820.2057386024651440.1776962037115560X-RAY DIFFRACTION100
2.8082-3.53780.1833109314631460.1743268472565636X-RAY DIFFRACTION100
3.5378-45.98040.181671632491520.1763427777385858X-RAY DIFFRACTION99.9168744805

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