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- PDB-1x0m: a Human Kynurenine Aminotransferase II Homologue from Pyrococcus ... -

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Basic information

Entry
Database: PDB / ID: 1x0m
Titlea Human Kynurenine Aminotransferase II Homologue from Pyrococcus horikoshii OT3
ComponentsAminotransferase II Homologue
KeywordsTRANSFERASE / aminotransferase
Function / homology
Function and homology information


alpha-amino acid metabolic process / transaminase activity / biosynthetic process / pyridoxal phosphate binding
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
Aminotransferase class I/classII domain-containing protein
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsChon, H. / Matsumura, H. / Koga, Y. / Takano, K. / Kanaya, S.
CitationJournal: Proteins / Year: 2005
Title: Crystal structure of a human kynurenine aminotransferase II homologue from Pyrococcus horikoshii OT3 at 2.20 A resolution
Authors: Chon, H. / Matsumura, H. / Koga, Y. / Takano, K. / Kanaya, S.
History
DepositionMar 24, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Aminotransferase II Homologue


Theoretical massNumber of molelcules
Total (without water)46,1051
Polymers46,1051
Non-polymers00
Water3,603200
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Aminotransferase II Homologue

A: Aminotransferase II Homologue


Theoretical massNumber of molelcules
Total (without water)92,2112
Polymers92,2112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area6960 Å2
ΔGint-35 kcal/mol
Surface area29920 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)71.751, 86.839, 137.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Aminotransferase II Homologue / hypothetical protein PH0207


Mass: 46105.363 Da / Num. of mol.: 1 / Fragment: Residues 26-428
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Production host: Escherichia coli (E. coli)
References: UniProt: O57946, kynurenine-oxoglutarate transaminase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.97 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Mar 3, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.2→55 Å / Num. obs: 22148 / Biso Wilson estimate: 29.4 Å2

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Processing

SoftwareName: CNS / Version: 1 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→43.42 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2281737.03 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1077 4.9 %RANDOM
Rwork0.212 ---
obs0.212 22117 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.3065 Å2 / ksol: 0.363876 e/Å3
Displacement parametersBiso mean: 44.8 Å2
Baniso -1Baniso -2Baniso -3
1-9.95 Å20 Å20 Å2
2---7.07 Å20 Å2
3----2.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.2→43.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3241 0 0 200 3441
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.341 184 5.1 %
Rwork0.252 3435 -
obs--99 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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