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- PDB-6hnu: Crystal structure of the aminotransferase Aro8 from C. Albicans w... -

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Basic information

Entry
Database: PDB / ID: 6hnu
TitleCrystal structure of the aminotransferase Aro8 from C. Albicans with ligands
ComponentsAromatic amino acid aminotransferase I
KeywordsTRANSFERASE / Aro8 from C. Albicans
Function / homology
Function and homology information


aromatic-amino-acid transaminase activity / aromatic-amino-acid transaminase / 2-aminoadipate transaminase activity / aromatic amino acid family catabolic process / L-tyrosine biosynthetic process / L-lysine biosynthetic process via aminoadipic acid / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
: / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHENYLALANINE / PYRIDOXAL-5'-PHOSPHATE / aromatic-amino-acid transaminase
Similarity search - Component
Biological speciesCandida albicans WO-1 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKiliszek, A. / Rzad, K. / Rypniewski, W. / Milewski, S. / Gabriel, I.
Funding support Poland, 1items
OrganizationGrant numberCountry
2015/17/B/NZ6/04248 Poland
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 1.1Mar 27, 2019Group: Data collection / Database references
Category: citation / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Jan 24, 2024Group: 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
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: Aromatic amino acid aminotransferase I
B: Aromatic amino acid aminotransferase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,24713
Polymers109,7402
Non-polymers1,50711
Water20,2671125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11600 Å2
ΔGint-94 kcal/mol
Surface area34330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.785, 102.090, 146.883
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 aminotransferase I


Mass: 54870.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans WO-1 (yeast) / Gene: CAWG_03814
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: C4YJ02

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Non-polymers , 6 types, 1136 molecules

#2: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO2
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1125 / 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: 2.38 Å3/Da / Density % sol: 48.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M MgCl2, 0.1 M Bis-Tris pH 5.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.8943 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8943 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 97014 / % possible obs: 99.6 % / Redundancy: 4.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.097 / Net I/σ(I): 11.29
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 15338 / CC1/2: 0.687 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HNB

6hnb


Resolution: 1.8→45.33 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.939 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21871 4851 5 %RANDOM
Rwork0.17362 ---
obs0.17587 92163 99.63 %-
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: 24.339 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20 Å2
2--0.28 Å2-0 Å2
3----0.6 Å2
Refinement stepCycle: 1 / Resolution: 1.8→45.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7577 0 94 1126 8797
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0137951
X-RAY DIFFRACTIONr_bond_other_d0.0350.0177383
X-RAY DIFFRACTIONr_angle_refined_deg1.5861.64710789
X-RAY DIFFRACTIONr_angle_other_deg2.2811.57517210
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9895968
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.24423.179390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.199151349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7651534
X-RAY DIFFRACTIONr_chiral_restr0.0850.21014
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028769
X-RAY DIFFRACTIONr_gen_planes_other0.0140.021643
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_it2.0122.3533856
X-RAY DIFFRACTIONr_mcbond_other22.3513854
X-RAY DIFFRACTIONr_mcangle_it2.8683.5114811
X-RAY DIFFRACTIONr_mcangle_other2.8743.5124812
X-RAY DIFFRACTIONr_scbond_it2.5432.6124095
X-RAY DIFFRACTIONr_scbond_other2.5432.6124096
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8613.8095971
X-RAY DIFFRACTIONr_long_range_B_refined5.74829.5619629
X-RAY DIFFRACTIONr_long_range_B_other5.56728.7759301
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.803→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 346 -
Rwork0.275 6583 -
obs--97.04 %

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