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- PDB-6hnb: Crystal structure of aminotransferase Aro8 from Candida albicans -

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Basic information

Entry
Database: PDB / ID: 6hnb
TitleCrystal structure of aminotransferase Aro8 from Candida albicans
ComponentsAromatic amino acid aminotransferase I
KeywordsTRANSFERASE / CaAro8
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 / 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
aromatic-amino-acid transaminase
Similarity search - Component
Biological speciesCandida albicans WO-1 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 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 14, 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)110,49310
Polymers109,7402
Non-polymers7528
Water17,078948
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10440 Å2
ΔGint-134 kcal/mol
Surface area34920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.371, 102.258, 147.051
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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
#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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 948 / 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: 2.41 Å3/Da / Density % sol: 48.98 %
Crystal growTemperature: 292 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: 14.3 / Wavelength: 0.895 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.895 Å / Relative weight: 1
ReflectionResolution: 1.96→50 Å / Num. obs: 76434 / % possible obs: 99.4 % / Redundancy: 7.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.148 / Net I/σ(I): 13.05
Reflection shellResolution: 1.96→2.08 Å / Redundancy: 7 % / Mean I/σ(I) obs: 2.03 / Num. unique obs: 11840 / CC1/2: 0.697 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JE5

4je5


Resolution: 1.96→48.29 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.509 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.157 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23294 2100 2.7 %RANDOM
Rwork0.17693 ---
obs0.17847 74317 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.991 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å2-0 Å20 Å2
2---0.59 Å20 Å2
3----0.4 Å2
Refinement stepCycle: 1 / Resolution: 1.96→48.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7577 0 42 948 8567
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0137839
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177272
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.64610623
X-RAY DIFFRACTIONr_angle_other_deg1.3291.57516942
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.065957
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.07123.057386
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53151332
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9331535
X-RAY DIFFRACTIONr_chiral_restr0.0780.2992
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028668
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021629
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_it1.9422.4573836
X-RAY DIFFRACTIONr_mcbond_other1.9412.4573835
X-RAY DIFFRACTIONr_mcangle_it2.8913.6744790
X-RAY DIFFRACTIONr_mcangle_other2.8913.6744791
X-RAY DIFFRACTIONr_scbond_it2.4152.7084003
X-RAY DIFFRACTIONr_scbond_other2.3822.7073996
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7623.9475821
X-RAY DIFFRACTIONr_long_range_B_refined5.38830.3079370
X-RAY DIFFRACTIONr_long_range_B_other5.25329.7129112
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.96→2.011 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 142 -
Rwork0.268 5052 -
obs--92.49 %

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