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- PDB-5a47: Structure of Thaumatin obtained by multi crystal data collection -

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Basic information

Entry
Database: PDB / ID: 5a47
TitleStructure of Thaumatin obtained by multi crystal data collection
ComponentsTHAUMATIN-1
KeywordsPLANT PROTEIN / MULTI CRYSTAL DATA COLLECTION / SYNCHROTRON SERIAL CRYSTALLOGRAPHY / SSX
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 / OTHER / Resolution: 1.2 Å
AuthorsZander, U. / Bourenkov, G. / Popov, A.N. / de Sanctis, D. / McCarthy, A.A. / Svensson, O. / Round, E.S. / Gordeliy, V.I. / Mueller-Dieckmann, C. / Leonard, G.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Meshandcollect: An Automated Multi-Crystal Data-Collection Workflow for Synchrotron Macromolecular Crystallography Beamlines.
Authors: Zander, U. / Bourenkov, G. / Popov, A.N. / De Sanctis, D. / Svensson, O. / Mccarthy, A.A. / Round, E. / Gordeliy, V. / Mueller-Dieckmann, C. / Leonard, G.A.
History
DepositionJun 5, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: THAUMATIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3772
Polymers22,2271
Non-polymers1501
Water5,224290
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.927, 57.927, 150.642
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.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / 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

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.73 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.969
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 1.19→19.76 Å / Num. obs: 81704 / % possible obs: 99.4 % / Observed criterion σ(I): 2.8 / Redundancy: 51.3 % / Rmerge(I) obs: 0.09

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Processing

SoftwareName: REFMAC / Version: 5.8.0103 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.2→20 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.944 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.15128 3972 4.9 %RANDOM
Rwork0.13294 ---
obs0.13383 77618 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.176 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20 Å2
2--0.29 Å20 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1551 0 10 290 1851
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.021709
X-RAY DIFFRACTIONr_bond_other_d0.0020.021514
X-RAY DIFFRACTIONr_angle_refined_deg2.1781.9562341
X-RAY DIFFRACTIONr_angle_other_deg2.17133519
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2355230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.15723.08868
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.77315259
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2731512
X-RAY DIFFRACTIONr_chiral_restr0.1560.2247
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212016
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02400
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_it1.2271.143884
X-RAY DIFFRACTIONr_mcbond_other1.1261.136883
X-RAY DIFFRACTIONr_mcangle_it1.5261.7181120
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4651.483825
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr12.17733223
X-RAY DIFFRACTIONr_sphericity_free23.329580
X-RAY DIFFRACTIONr_sphericity_bonded7.11553374
LS refinement shellResolution: 1.195→1.226 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.212 263 -
Rwork0.197 5246 -
obs--92.42 %

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