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- PDB-6hnv: Crystal structure of aminotransferase Aro9 from C. Albicans with ... -

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Basic information

Entry
Database: PDB / ID: 6hnv
TitleCrystal structure of aminotransferase Aro9 from C. Albicans with ligands
ComponentsAromatic-amino-acid:2-oxoglutarate transaminase
KeywordsTRANSFERASE / Aro9 from C. Albicans
Function / homology
Function and homology information


kynurenine aminotransferase activity / aromatic-amino-acid:2-oxoglutarate aminotransferase activity / L-lysine catabolic process / aromatic amino acid family catabolic process to alcohol via Ehrlich pathway / 2-aminoadipate transaminase activity / alpha-amino acid metabolic process / aromatic amino acid family catabolic process / tyrosine biosynthetic process / lysine biosynthetic process via aminoadipic acid / L-phenylalanine biosynthetic process ...kynurenine aminotransferase activity / aromatic-amino-acid:2-oxoglutarate aminotransferase activity / L-lysine catabolic process / aromatic amino acid family catabolic process to alcohol via Ehrlich pathway / 2-aminoadipate transaminase activity / alpha-amino acid metabolic process / aromatic amino acid family catabolic process / tyrosine biosynthetic process / lysine biosynthetic process via aminoadipic acid / L-phenylalanine biosynthetic process / transaminase activity / aromatic amino acid family biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
Aminotransferase, class I/classII / Aminotransferase class I and II / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
2-OXOADIPIC ACID / PHENYLALANINE / PYRIDOXAL-5'-PHOSPHATE / 3-PHENYLPYRUVIC ACID / 2-AMINOHEXANEDIOIC ACID / Aromatic-amino-acid:2-oxoglutarate transaminase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKiliszek, A. / Rzad, K. / Rypniewski, W. / Milewski, S. / Gabriel, I.
Funding support1items
OrganizationGrant numberCountry
2015/17/B/NZ6/04248
CitationJournal: J.Struct.Biol. / Year: 2019
Title: Crystal structures of aminotransferases Aro8 and Aro9 from Candida albicans and structural insights into their properties.
Authors: Kiliszek, A. / Rypniewski, W. / Rzad, K. / Milewski, S. / Gabriel, I.
History
DepositionSep 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 2.0Mar 6, 2019Group: Atomic model / Data collection / Derived calculations
Category: atom_site / struct_conn ...atom_site / struct_conn / struct_site / struct_site_gen
Item: _atom_site.label_alt_id
Revision 2.1Mar 27, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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: Aromatic-amino-acid:2-oxoglutarate transaminase
B: Aromatic-amino-acid:2-oxoglutarate transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,79512
Polymers118,0432
Non-polymers1,75310
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12230 Å2
ΔGint-59 kcal/mol
Surface area35150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.570, 88.540, 160.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Aromatic-amino-acid:2-oxoglutarate transaminase


Mass: 59021.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Gene: ARO9, orf19.1237, CAALFM_C405560CA
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A1D8PMC5

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Non-polymers , 8 types, 205 molecules

#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: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO2
#6: Chemical ChemComp-PPY / 3-PHENYLPYRUVIC ACID


Mass: 164.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8O3
#7: Chemical ChemComp-UN1 / 2-AMINOHEXANEDIOIC ACID


Type: L-peptide linking / Mass: 161.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11NO4
#8: Chemical ChemComp-OOG / 2-OXOADIPIC ACID


Mass: 160.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O5
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.24 Å3/Da / Density % sol: 45.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.06 M MgCl2, 0.06 M CaCl2, 0.1 M Tris (base): BICINE pH 8.5, 12.5% v/v MPD, 12.5% PEG 1000, 12.5% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.89429 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89429 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 31584 / % possible obs: 94 % / Redundancy: 4.7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.178 / Net I/σ(I): 9.22
Reflection shellResolution: 2.6→2.76 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.904 / Mean I/σ(I) obs: 2.05 / Num. unique obs: 5145 / CC1/2: 0.717 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→46.53 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.881 / Cross valid method: THROUGHOUT / ESU R Free: 0.379 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27971 948 3 %RANDOM
Rwork0.19917 ---
obs0.20159 30634 93.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 46.982 Å2
Baniso -1Baniso -2Baniso -3
1-1.69 Å20 Å20 Å2
2--0.11 Å2-0 Å2
3----1.81 Å2
Refinement stepCycle: 1 / Resolution: 2.6→46.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7530 0 117 195 7842
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0137842
X-RAY DIFFRACTIONr_bond_other_d0.0340.0177233
X-RAY DIFFRACTIONr_angle_refined_deg1.5841.64810634
X-RAY DIFFRACTIONr_angle_other_deg2.3051.58116804
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5035926
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.09723.081409
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.104151292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4071535
X-RAY DIFFRACTIONr_chiral_restr0.0690.2990
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028644
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021651
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_it3.6124.8593731
X-RAY DIFFRACTIONr_mcbond_other3.6134.8593730
X-RAY DIFFRACTIONr_mcangle_it5.3987.2694648
X-RAY DIFFRACTIONr_mcangle_other5.3977.274649
X-RAY DIFFRACTIONr_scbond_it3.7295.224111
X-RAY DIFFRACTIONr_scbond_other3.7295.2214112
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7227.7025987
X-RAY DIFFRACTIONr_long_range_B_refined7.76756.2348595
X-RAY DIFFRACTIONr_long_range_B_other7.76356.2248588
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.599→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 70 -
Rwork0.278 2263 -
obs--95.15 %

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