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- PDB-5jvx: X-ray structure of the adduct formed in the reaction between thau... -

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Basic information

Entry
Database: PDB / ID: 5jvx
TitleX-ray structure of the adduct formed in the reaction between thaumatin and a gold carbene compound
ComponentsThaumatin-1
KeywordsPLANT PROTEIN
Function / homology
Function and homology information


cytoplasmic vesicle
Similarity search - Function
Thaumatin / Thaumatin / Thaumatin, conserved site / Thaumatin family signature. / Thaumatin family / Thaumatin family / Thaumatin family profile. / Thaumatin family / Osmotin/thaumatin-like superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-6O0 / L(+)-TARTARIC ACID / Thaumatin I
Similarity search - Component
Biological speciesThaumatococcus daniellii (katemfe)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsFerraro, G. / Merlino, A.
CitationJournal: Bioconjug.Chem. / Year: 2016
Title: First Crystal Structure for a Gold Carbene-Protein Adduct.
Authors: Ferraro, G. / Gabbiani, C. / Merlino, A.
History
DepositionMay 11, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thaumatin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,78610
Polymers22,2271
Non-polymers2,5599
Water5,639313
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area480 Å2
ΔGint-6 kcal/mol
Surface area9780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.912, 57.912, 150.136
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Thaumatin-1 / Thaumatin I


Mass: 22227.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thaumatococcus daniellii (katemfe) / References: UniProt: P02883
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical
ChemComp-6O0 / (1-butyl-3-methyl-1,3-dihydro-2H-imidazol-2-ylidene)(chloro)gold


Mass: 370.630 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H14AuClN2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.83 Å3/Da / Density % sol: 56.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.2 M sodium tartrate pH 7.2, 20 % polyethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Dec 21, 2015 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→57.91 Å / Num. obs: 27058 / % possible obs: 93 % / Redundancy: 20.9 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 37
Reflection shellHighest resolution: 1.7 Å / Rmerge(I) obs: 1.74 / Mean I/σ(I) obs: 1.7 / CC1/2: 0.59 / Rpim(I) all: 0.48

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QY5

3qy5


Resolution: 1.7→54.03 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.899 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.093 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.1874 1323 4.9 %RANDOM
Rwork0.16988 ---
obs0.17076 25708 93.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.949 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å2-0 Å2-0 Å2
2--0.13 Å2-0 Å2
3----0.25 Å2
Refinement stepCycle: 1 / Resolution: 1.7→54.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1551 0 57 313 1921
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021758
X-RAY DIFFRACTIONr_bond_other_d0.0030.021533
X-RAY DIFFRACTIONr_angle_refined_deg1.3851.9822403
X-RAY DIFFRACTIONr_angle_other_deg0.9433.0023562
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4165228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.1122.81771
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.59615263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7711514
X-RAY DIFFRACTIONr_chiral_restr0.0780.2246
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212071
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02397
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_it1.1912.118876
X-RAY DIFFRACTIONr_mcbond_other1.1872.114875
X-RAY DIFFRACTIONr_mcangle_it1.9423.1731110
X-RAY DIFFRACTIONr_mcangle_other1.9443.1771111
X-RAY DIFFRACTIONr_scbond_it1.7022.358882
X-RAY DIFFRACTIONr_scbond_other1.7012.358883
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8623.4511296
X-RAY DIFFRACTIONr_long_range_B_refined7.32620.2352275
X-RAY DIFFRACTIONr_long_range_B_other7.3520.132258
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 78 -
Rwork0.277 1619 -
obs--80.81 %

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