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- PDB-3av7: Crystal structure of Pyrococcus horikoshii kynurenine aminotransf... -

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Basic information

Entry
Database: PDB / ID: 3av7
TitleCrystal structure of Pyrococcus horikoshii kynurenine aminotransferase in complex with PMP, KYN as substrates and KYA as products
ComponentsPutative uncharacterized protein PH0207
KeywordsTRANSFERASE / 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 / 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
4-hydroxyquinoline-2-carboxylic acid / (2S)-2-amino-4-(2-aminophenyl)-4-oxobutanoic acid / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / Aminotransferase class I/classII domain-containing protein
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsOkada, K. / Angkawidjaja, C. / Koga, Y. / Takano, K. / Kanaya, S.
CitationJournal: To be Published
Title: Structural insight into kynurenic acid excretion mechanisms of kynurenine aminotransferase in the hyperthermophilic archaeon Pyrococcus horikoshii
Authors: Okada, K. / Angkawidjaja, C. / Koga, Y. / Takano, K. / Kanaya, Y.
History
DepositionFeb 23, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 7, 2012Provider: 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)103,6178
Polymers102,3262
Non-polymers1,2916
Water9,998555
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7100 Å2
ΔGint-38 kcal/mol
Surface area29920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.619, 136.529, 55.612
Angle α, β, γ (deg.)90.00, 100.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative uncharacterized protein PH0207 / kynurneine 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-CodonPlus (DE3)
References: UniProt: O57946, kynurenine-oxoglutarate transaminase
#2: Chemical ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13N2O5P
#3: Chemical ChemComp-KYN / (2S)-2-amino-4-(2-aminophenyl)-4-oxobutanoic acid / L-KYNURENINE


Type: L-peptide linking / Mass: 208.214 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N2O3
#4: Chemical ChemComp-KYA / 4-hydroxyquinoline-2-carboxylic acid / Kynurenic acid


Mass: 189.167 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H7NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 555 / 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: 39.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M imidazole pH 8.0, 0.2M calcium acetate, 20% w/v polyethylene glycol 1000, 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: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 24, 2010 / Details: mirrors
RadiationMonochromator: Rh mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.84→40 Å / Num. obs: 67298 / % possible obs: 93.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.081
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 1.49 / % possible all: 96.7

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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 3AOV

3aov


Resolution: 1.84→26.69 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.34 / SU ML: 0.101 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2379 3411 5.1 %RANDOM
Rwork0.17618 ---
obs0.17929 63854 95.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å22.2 Å2
2---0.02 Å20 Å2
3---0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.84→26.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6494 0 90 555 7139
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0226718
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0192.0029058
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9075806
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.31824.286294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.559151262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8851542
X-RAY DIFFRACTIONr_chiral_restr0.1470.2976
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0215014
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_it1.2071.54022
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.05126510
X-RAY DIFFRACTIONr_scbond_it3.44732696
X-RAY DIFFRACTIONr_scangle_it5.4244.52548
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.841→1.889 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 224 -
Rwork0.263 4415 -
obs--90.38 %

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