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- PDB-6hnd: Crystal structure of the aromatic aminotransferase Aro9 from C. A... -

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Basic information

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


: / aromatic-amino-acid transaminase activity / L-lysine catabolic process / aromatic amino acid family catabolic process to alcohol via Ehrlich pathway / 2-aminoadipate transaminase activity / aromatic amino acid family catabolic process / tyrosine biosynthetic process / lysine biosynthetic process via aminoadipic acid / L-phenylalanine biosynthetic process / 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
: / PYRIDOXAL-5'-PHOSPHATE / Aromatic-amino-acid:2-oxoglutarate transaminase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 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
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)120,1947
Polymers119,4242
Non-polymers7705
Water9,368520
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11180 Å2
ΔGint-73 kcal/mol
Surface area35610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.377, 89.285, 161.908
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:2-oxoglutarate transaminase


Mass: 59712.059 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast)
Strain: SC5314 / ATCC MYA-2876 / Gene: ARO9, orf19.1237, CAALFM_C405560CA
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A1D8PMC5
#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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 520 / 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: 2.3 Å3/Da / Density % sol: 46.5 %
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: Jan 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89429 Å / Relative weight: 1
ReflectionResolution: 2.23→50 Å / Num. obs: 53903 / % possible obs: 99.7 % / Redundancy: 6 % / Rmerge(I) obs: 0.154 / Net I/σ(I): 11.3
Reflection shellResolution: 2.23→2.36 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.919 / Mean I/σ(I) obs: 2.19 / Num. unique obs: 8523 / CC1/2: 0.788 / % possible all: 99.1

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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: 2.23→46.93 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.932 / SU B: 6.999 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.253 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23024 2696 5 %RANDOM
Rwork0.16891 ---
obs0.17193 51206 99.7 %-
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: 41.075 Å2
Baniso -1Baniso -2Baniso -3
1-2.37 Å20 Å20 Å2
2---0.36 Å20 Å2
3----2.01 Å2
Refinement stepCycle: 1 / Resolution: 2.23→46.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7557 0 47 520 8124
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0137797
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177190
X-RAY DIFFRACTIONr_angle_refined_deg1.5171.64510588
X-RAY DIFFRACTIONr_angle_other_deg1.2711.57916700
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0585929
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.00423.243407
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.667151290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4181534
X-RAY DIFFRACTIONr_chiral_restr0.0710.2991
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028611
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021641
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_it3.1624.1433740
X-RAY DIFFRACTIONr_mcbond_other3.164.1423739
X-RAY DIFFRACTIONr_mcangle_it4.4896.194661
X-RAY DIFFRACTIONr_mcangle_other4.4896.1914662
X-RAY DIFFRACTIONr_scbond_it3.8754.5594057
X-RAY DIFFRACTIONr_scbond_other3.8744.564058
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8216.6825928
X-RAY DIFFRACTIONr_long_range_B_refined7.39548.3338794
X-RAY DIFFRACTIONr_long_range_B_other7.40148.1728709
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.23→2.288 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 194 -
Rwork0.264 3678 -
obs--98.2 %

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