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- PDB-2rkv: Crystal Structure of F. graminearum TRI101 complexed with Coenzym... -

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Basic information

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


transferase activity / metal ion binding
Similarity search - Function
Trichothecene 3-O-acetyltransferase-like N-terminal domain / : / Transferase family / Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain / Chloramphenicol acetyltransferase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Chem-ZBA / Trichothecene 3-O-acetyltransferase / Trichothecene 3-O-acetyltransferase
Similarity search - Component
Biological speciesGibberella zeae (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsGarvey, G.S. / 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 17, 2007Deposition site: RCSB / 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 1.3Aug 30, 2023Group: 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8904
Polymers49,4491
Non-polymers1,4413
Water10,016556
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)123.113, 123.113, 81.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-455-

HOH

21A-688-

HOH

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Components

#1: Protein Trichothecene 3-O-acetyltransferase


Mass: 49449.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gibberella zeae (fungus) / Strain: PH-1 / 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: Q9HDE2, UniProt: O42692*PLUS
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID


Mass: 209.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#4: 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.: 1 / Source method: obtained synthetically / Formula: C24H32O9
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 556 / 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: 3.11 Å3/Da / Density % sol: 60.5 %
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: 0.97907 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 78126 / % possible obs: 86.4 % / Redundancy: 5.8 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 20.2
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 1.2 / % possible all: 46.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2zba

2zba


Resolution: 1.6→33.9 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.472 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20896 3596 5 %RANDOM
Rwork0.18412 ---
obs0.18537 67669 86.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.061 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2--0.1 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.6→33.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3385 0 91 556 4032
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223650
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2012.0035000
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3145473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.92523.946147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.2315599
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5781524
X-RAY DIFFRACTIONr_chiral_restr0.0790.2561
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022751
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.21910
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22534
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.2471
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.227
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1010.232
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5151.52322
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.86423673
X-RAY DIFFRACTIONr_scbond_it1.32731495
X-RAY DIFFRACTIONr_scangle_it2.0954.51309
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 129 -
Rwork0.349 2521 -
obs--43.89 %

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