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- PDB-6fj9: Structure of Thaumatin collected from an in situ crystal on ID30B... -

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Basic information

Entry
Database: PDB / ID: 6fj9
TitleStructure of Thaumatin collected from an in situ crystal on ID30B at 17.5 keV.
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
L(+)-TARTARIC ACID / Thaumatin I
Similarity search - Component
Biological speciesThaumatococcus daniellii (katemfe)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMcCarthy, A.A. / Mueller-Dieckmann, C.
CitationJournal: J Synchrotron Radiat / Year: 2018
Title: ID30B - a versatile beamline for macromolecular crystallography experiments at the ESRF.
Authors: McCarthy, A.A. / Barrett, R. / Beteva, A. / Caserotto, H. / Dobias, F. / Felisaz, F. / Giraud, T. / Guijarro, M. / Janocha, R. / Khadrouche, A. / Lentini, M. / Leonard, G.A. / Lopez Marrero, ...Authors: McCarthy, A.A. / Barrett, R. / Beteva, A. / Caserotto, H. / Dobias, F. / Felisaz, F. / Giraud, T. / Guijarro, M. / Janocha, R. / Khadrouche, A. / Lentini, M. / Leonard, G.A. / Lopez Marrero, M. / Malbet-Monaco, S. / McSweeney, S. / Nurizzo, D. / Papp, G. / Rossi, C. / Sinoir, J. / Sorez, C. / Surr, J. / Svensson, O. / Zander, U. / Cipriani, F. / Theveneau, P. / Mueller-Dieckmann, C.
History
DepositionJan 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 8, 2018Group: Data collection / Database references / Category: citation_author / pdbx_related_exp_data_set
Item: _citation_author.identifier_ORCID / _pdbx_related_exp_data_set.data_reference
Revision 1.3Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 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)22,3772
Polymers22,2271
Non-polymers1501
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint2 kcal/mol
Surface area9680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.570, 58.570, 151.544
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 genetically manipulated source
Source: (gene. exp.) Thaumatococcus daniellii (katemfe) / Production host: Thaumatococcus daniellii (katemfe) / References: UniProt: P02883
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.93 Å3/Da / Density % sol: 58 % / Description: Bipyramidal crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES and 0.7 M potassium/sodium tartrate

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.7085 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 12, 2016
Details: Be CRL (vertical focusing) and Rh stripe Elliptical mirror (horizontal focusing)
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7085 Å / Relative weight: 1
ReflectionResolution: 1.5→54.63 Å / Num. obs: 39794 / % possible obs: 92.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 12.4 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.057 / Rrim(I) all: 0.111 / Net I/σ(I): 7.2
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.727 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1988 / CC1/2: 0.6 / Rpim(I) all: 0.518 / Rrim(I) all: 0.979 / % possible all: 96.7

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Processing

Software
NameVersionClassification
MxCuBE2.2data collection
REFMAC5.8.0189refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5a47

5a47


Resolution: 1.5→54.63 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.973 / SU B: 2.533 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.056 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16678 1985 5 %RANDOM
Rwork0.13673 ---
obs0.1382 37747 92.02 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 19.775 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0 Å2-0 Å2
2--0.04 Å2-0 Å2
3----0.08 Å2
Refinement stepCycle: 1 / Resolution: 1.5→54.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1545 0 10 121 1676
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021660
X-RAY DIFFRACTIONr_bond_other_d0.0020.021472
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.962274
X-RAY DIFFRACTIONr_angle_other_deg0.92433445
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.8265.109229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.34923.28467
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.98715257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.251512
X-RAY DIFFRACTIONr_chiral_restr0.0870.2246
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211896
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02356
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_it1.1431.737845
X-RAY DIFFRACTIONr_mcbond_other1.0851.734844
X-RAY DIFFRACTIONr_mcangle_it1.542.6161060
X-RAY DIFFRACTIONr_mcangle_other1.5522.6181061
X-RAY DIFFRACTIONr_scbond_it1.5262.052815
X-RAY DIFFRACTIONr_scbond_other1.5292.054812
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9722.9471202
X-RAY DIFFRACTIONr_long_range_B_refined2.28620.7311754
X-RAY DIFFRACTIONr_long_range_B_other2.28420.6711748
X-RAY DIFFRACTIONr_rigid_bond_restr1.97533132
X-RAY DIFFRACTIONr_sphericity_free22.123597
X-RAY DIFFRACTIONr_sphericity_bonded8.75653100
LS refinement shellResolution: 1.501→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 176 -
Rwork0.264 2830 -
obs--96.22 %

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