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- PDB-2zba: Crystal Structure of F. sporotrichioides TRI101 complexed with Co... -

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Basic information

Entry
Database: PDB / ID: 2zba
TitleCrystal Structure of F. sporotrichioides TRI101 complexed with Coenzyme A and T-2
ComponentsTrichothecene 3-O-acetyltransferase
KeywordsTRANSFERASE / acetyltransferase / BAHD superfamily / trichothecene / deoxynivalenol / T-2 / acetyl CoA / Fusarium / TRI101
Function / homology
Function and homology information


Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / transferase activity / metal ion binding
Similarity search - Function
: / Trichothecene 3-O-acetyltransferase-like N-terminal domain / : / Transferase family / Chloramphenicol acetyltransferase-like domain / Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Chem-ZBA / Trichothecene 3-O-acetyltransferase TRI101
Similarity search - Component
Biological speciesFusarium sporotrichioides (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å
AuthorsGarvey, G.S. / McCormick, S.P. / Rayment, I.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structural and Functional Characterization of the TRI101 Trichothecene 3-O-Acetyltransferase from Fusarium sporotrichioides and Fusarium graminearum: KINETIC INSIGHTS TO COMBATING FUSARIUM HEAD BLIGHT
Authors: Garvey, G.S. / McCormick, S.P. / Rayment, I.
History
DepositionOct 18, 2007Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Dec 21, 2016Group: Structure summary
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_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_asym_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_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trichothecene 3-O-acetyltransferase
B: Trichothecene 3-O-acetyltransferase
C: Trichothecene 3-O-acetyltransferase
D: Trichothecene 3-O-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,17316
Polymers203,9944
Non-polymers5,17912
Water16,430912
1
A: Trichothecene 3-O-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3115
Polymers50,9991
Non-polymers1,3124
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Trichothecene 3-O-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3094
Polymers50,9991
Non-polymers1,3103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Trichothecene 3-O-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3234
Polymers50,9991
Non-polymers1,3243
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Trichothecene 3-O-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2313
Polymers50,9991
Non-polymers1,2322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.973, 81.966, 113.506
Angle α, β, γ (deg.)90.00, 109.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Trichothecene 3-O-acetyltransferase


Mass: 50998.559 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusarium sporotrichioides (fungus) / Gene: TRI101 / Plasmid details: rTEV cleavable N terminal His Tag / Plasmid: pET31b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: O94197

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Non-polymers , 6 types, 924 molecules

#2: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical
ChemComp-ZBA / 12,13-Epoxytrichothec-9-ene-3,4,8,15-tetrol-4,15-diacetate-8-isovalerate


Mass: 464.505 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H32O9
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 912 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 2.1M sodium malonate, 100 mM 3-N-morpholino propanesulfonic acid, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: .97907,.97924
DetectorDetector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979071
20.979241
ReflectionResolution: 2→50 Å / Num. obs: 118024 / % possible obs: 89.2 % / Redundancy: 1.6 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 8.9
Reflection shellResolution: 2→2.08 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 1.7 / % possible all: 74.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.909 / SU B: 4.603 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.241 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2505 5205 5 %RANDOM
Rwork0.19854 ---
obs0.20114 99193 88.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.213 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20.15 Å2
2---0.35 Å20 Å2
3---0.61 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12793 0 333 912 14038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02213463
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4982.00718320
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9451684
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.65623.626513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.129152153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0141590
X-RAY DIFFRACTIONr_chiral_restr0.10.22058
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029977
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.26548
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.29078
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.21023
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1850.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.264
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0250.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7191.58683
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.144213547
X-RAY DIFFRACTIONr_scbond_it1.77235448
X-RAY DIFFRACTIONr_scangle_it2.5044.54751
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 303 -
Rwork0.232 5991 -
obs--72.81 %

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