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- PDB-3aov: Crystal structure of Pyrococcus horikoshii kynurenine aminotransf... -

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Basic information

Entry
Database: PDB / ID: 3aov
TitleCrystal structure of Pyrococcus horikoshii kynurenine aminotransferase in complex with PLP
ComponentsPutative uncharacterized protein PH0207
KeywordsTRANSFERASE / Protein-PLP complex / Schiff-base linkage / Kynurenin aminotransferase / Cofactor complex / aminotransferase / PLP binding / Transamination
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 ...: / 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
PYRIDOXAL-5'-PHOSPHATE / Aminotransferase class I/classII large domain-containing protein
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsOkada, K. / Angkawidjaja, C. / Koga, Y. / Takano, K. / Kanaya, S.
CitationJournal: To be Published
Title: Characterization of kynurenine aminotransferase from hyperthermophilic archaeon: enzymatic activity for conversion to kynurenic acid is allosterically regulated by alpha-ketoglutaric acid ...Title: Characterization of kynurenine aminotransferase from hyperthermophilic archaeon: enzymatic activity for conversion to kynurenic acid is allosterically regulated by alpha-ketoglutaric acid cooperatively with kynurenine
Authors: Okada, K. / Angkawidjaja, C. / Koga, Y. / Takano, K. / Kanaya, Y.
History
DepositionOct 7, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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: Putative uncharacterized protein PH0207
C: Putative uncharacterized protein PH0207
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,8204
Polymers102,3262
Non-polymers4942
Water10,539585
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-38 kcal/mol
Surface area29910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.927, 71.055, 136.348
Angle α, β, γ (deg.)90.00, 89.99, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Putative uncharacterized protein PH0207 / Kynurenine aminotransferase


Mass: 51162.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH0207 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: O57946, kynurenine-oxoglutarate transaminase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 585 / 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: 2.03 Å3/Da / Density % sol: 39.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M magnesium chloride hexahydrate, 0.1M HEPES sodium pH7.5, 30% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 8, 2010 / Details: mirrors
RadiationMonochromator: Rh mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.72→50 Å / Num. obs: 86393 / % possible obs: 99.2 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.071 / Rsym value: 0.063 / Net I/σ(I): 31.6
Reflection shellHighest resolution: 1.72 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.567 / Mean I/σ(I) obs: 2.75 / Num. unique all: 4357 / Rsym value: 0.415 / % possible all: 100

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Processing

Software
NameVersionClassification
BL38B1BSS softwaredata collection
MOLREPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1X0M

1x0m


Resolution: 1.72→26.84 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.569 / SU ML: 0.084 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23156 4333 5 %RANDOM
Rwork0.18371 ---
obs0.18611 82018 98.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.879 Å2
Baniso -1Baniso -2Baniso -3
1--2.21 Å20 Å2-0.11 Å2
2--3.29 Å20 Å2
3----1.08 Å2
Refinement stepCycle: LAST / Resolution: 1.72→26.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6494 0 30 585 7109
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0226656
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1211.9938974
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7745806
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.15124.286294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.884151262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5971542
X-RAY DIFFRACTIONr_chiral_restr0.1510.2974
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0214942
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3971.54018
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.31526502
X-RAY DIFFRACTIONr_scbond_it3.46132638
X-RAY DIFFRACTIONr_scangle_it5.6344.52472
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.719→1.764 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 319 -
Rwork0.266 5883 -
obs--96.94 %

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