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- PDB-6s8w: Aromatic aminotransferase AroH (Aro8) form Aspergillus fumigatus ... -

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Basic information

Entry
Database: PDB / ID: 6s8w
TitleAromatic aminotransferase AroH (Aro8) form Aspergillus fumigatus in complex with PLP (internal aldimine)
ComponentsAromatic aminotransferase Aro8, putative
KeywordsTRANSFERASE / AMINOTRANSFERASE / PLP / metabolism / amino acid / fungi
Function / homology
Function and homology information


aromatic-amino-acid transaminase activity / 2-aminoadipate transaminase activity / aromatic amino acid family catabolic process / L-tyrosine biosynthetic process / L-lysine biosynthetic process via aminoadipic acid / Transferases; Transferring nitrogenous groups; Transaminases / 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
FORMIC ACID / PYRIDOXAL-5'-PHOSPHATE / Aromatic aminotransferase Aro8, putative
Similarity search - Component
Biological speciesAspergillus fumigatus Af293 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsGiardina, G. / Mirco, D. / Spizzichino, S. / Zelante, T. / Cutruzzola, F. / Romani, L. / Cellini, B.
Funding support Italy, 4items
OrganizationGrant numberCountry
Italian Ministry of EducationRP11715C644A5CCE Italy
Italian Ministry of EducationRG11816430AF48E1 Italy
Italian Ministry of EducationPGR13XNIDJ Italy
European Research CouncilERC-2011-AdG-293714 Italy
CitationJournal: Proteins / Year: 2021
Title: Crystal structure of Aspergillus fumigatus AroH, an aromatic amino acid aminotransferase
Authors: Spizzichino, S. / Pampalone, G. / Dindo, M. / Bruno, A. / Romani, L. / Cutruzzola, F. / Zelante, T. / Pieroni, M. / Cellini, B. / Giardina, G.
History
DepositionJul 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 15, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aromatic aminotransferase Aro8, putative
B: Aromatic aminotransferase Aro8, putative
C: Aromatic aminotransferase Aro8, putative
D: Aromatic aminotransferase Aro8, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,92310
Polymers236,8434
Non-polymers1,0816
Water2,990166
1
A: Aromatic aminotransferase Aro8, putative
B: Aromatic aminotransferase Aro8, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,9625
Polymers118,4212
Non-polymers5403
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Aromatic aminotransferase Aro8, putative
D: Aromatic aminotransferase Aro8, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,9625
Polymers118,4212
Non-polymers5403
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.209, 75.260, 121.631
Angle α, β, γ (deg.)84.770, 87.510, 65.370
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / Refine code: 1

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERAA16 - 52516 - 525
21SERSERBB16 - 52516 - 525
12GLUGLUAA16 - 52316 - 523
22GLUGLUCC16 - 52316 - 523
13SERSERAA16 - 52516 - 525
23SERSERDD16 - 52516 - 525
14GLUGLUBB16 - 52316 - 523
24GLUGLUCC16 - 52316 - 523
15LEULEUBB16 - 52616 - 526
25LEULEUDD16 - 52616 - 526
16GLUGLUCC16 - 52316 - 523
26GLUGLUDD16 - 52316 - 523

NCS ensembles :
ID
1
2
3
4
5
6

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.802843, -0.379069, -0.460163), (-0.394198, -0.916559, 0.067281), (-0.447271, 0.12738, -0.885282)-9.29758, -33.593979, -8.47781
3given(1), (1), (1)
4given(0.354652, 0.478926, -0.803027), (0.45948, -0.837266, -0.296419), (-0.814309, -0.263849, -0.516995)57.18969, 8.08257, -7.40194
5given(1), (1), (1)
6given(0.484224, 0.819689, -0.306002), (-0.617338, 0.567917, 0.544394), (0.620017, -0.074702, 0.781024)37.510071, -63.390511, -26.095301
7given(1), (1), (1)
8given(0.468262, 0.832452, -0.296234), (-0.65614, 0.552142, 0.514412), (0.591787, -0.046509, 0.804752)36.466759, -63.425571, -28.595289
9given(1), (1), (1)
10given(0.356665, 0.471333, -0.80662), (0.464731, -0.83851, -0.284476), (-0.810441, -0.273399, -0.51811)57.057949, 7.55316, -7.48964
11given(1), (1), (1)
12given(-0.616819, 0.609478, -0.498067), (0.589917, -0.060956, -0.80516), (-0.521087, -0.790456, -0.321942)-24.401871, 55.373611, 47.051769

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Components

#1: Protein
Aromatic aminotransferase Aro8, putative


Mass: 59210.680 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: pyridoxal 5'-phosphate (PLP) bound to K348 through a Schiff base linkage
Source: (gene. exp.) Aspergillus fumigatus Af293 (mold) / Gene: AFUA_2G13630 / Plasmid: pET22b(+) / Details (production host): C-terminal histidine tag / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q4X0F7, Transferases; Transferring nitrogenous groups; Transaminases
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.28 Å3/Da / Density % sol: 46.03 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 6.5
Details: Optimization of hit G4 of the Molecular Dimension Morpheus screen : 0.1M (Sodium formate; Ammonium acetate; Sodium citrate tribasic dihydrate; Potassium sodium tartrate tetrahydrate; Sodium ...Details: Optimization of hit G4 of the Molecular Dimension Morpheus screen : 0.1M (Sodium formate; Ammonium acetate; Sodium citrate tribasic dihydrate; Potassium sodium tartrate tetrahydrate; Sodium oxamate); 50mM Imidazole; 50mMES monohydrate (acid); 13.7% v/v MPD; 13.7% PEG 1000; 13.7% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 16, 2019
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→47.2 Å / Num. obs: 78375 / % possible obs: 97.2 % / Redundancy: 3.8 % / CC1/2: 0.992 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.065 / Rrim(I) all: 0.127 / Net I/σ(I): 6.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.4-2.4540.7811817945420.5970.4510.9041.497.5
12.24-47.23.40.08819055680.980.0550.10513.193.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.596
Highest resolutionLowest resolution
Rotation47.21 Å2.76 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0238refinement
XDSdata reduction
Aimless0.7.4data scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JE5

4je5


Resolution: 2.4→47.2 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.901 / SU R Cruickshank DPI: 0.5887 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.589 / ESU R Free: 0.322
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2935 3871 4.9 %RANDOM
Rwork0.2455 ---
obs0.248 74503 97.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 118.94 Å2 / Biso mean: 52.302 Å2 / Biso min: 28.39 Å2
Baniso -1Baniso -2Baniso -3
1-4.56 Å20.48 Å20.03 Å2
2---0.82 Å2-0.16 Å2
3----2.93 Å2
Refinement stepCycle: final / Resolution: 2.4→47.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14565 0 6 166 14737
Biso mean--50.78 47.2 -
Num. residues----1940
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01314968
X-RAY DIFFRACTIONr_bond_other_d0.0360.01713208
X-RAY DIFFRACTIONr_angle_refined_deg1.2241.64420426
X-RAY DIFFRACTIONr_angle_other_deg2.4361.56530435
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.33351922
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.80521.036676
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.589152062
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2341592
X-RAY DIFFRACTIONr_chiral_restr0.0590.21972
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0217027
X-RAY DIFFRACTIONr_gen_planes_other0.0040.023293
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.87

Ens-IDAuth asym-IDNumberRms dev position (Å)
1A35713.85
2A34738.75
3A349612.21
4B33789.24
5B358311.34
6C33228.6
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 317 -
Rwork0.356 5497 -
all-5814 -
obs--97.47 %

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