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- PDB-6coa: 1.2 A Structure of Thaumatin Crystallized in Gel -

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Basic information

Entry
Database: PDB / ID: 6coa
Title1.2 A Structure of Thaumatin Crystallized in Gel
ComponentsThaumatin-1
KeywordsPLANT PROTEIN / Sweet tasting protein / agarose gel / microgravity / APCF
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: 1.2 Å
AuthorsSauter, C. / Lorber, B. / Shabalin, I.G. / Porebski, P.J. / Brzezinski, D. / Giege, R.
Funding support France, 5items
OrganizationGrant numberCountry
CNRS France
Universite Louis Pasteur Strasbourg France
CNES (France) France
ESA France
EU project European Bio-Crystallogenesis InitiativeBIO4-CT98-0086 France
Citation
Journal: Proteins / Year: 2002
Title: Towards atomic resolution with crystals grown in gel: the case of thaumatin seen at room temperature.
Authors: Sauter, C. / Lorber, B. / Giege, R.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 1999
Title: Crystallization within agarose gel in microgravity improves the quality of thaumatin crystals.
Authors: Lorber, B. / Sauter, C. / Robert, M.C. / Capelle, B. / Giege, R.
#2: Journal: Bioinformatics / Year: 2018
Title: Automatic Recognition of Ligands in Electron Density by Machine Learning.
Authors: Kowiel, M. / Brzezinski, D. / Porebski, P.J. / Shabalin, I.G. / Jaskolski, M. / Minor, W.
History
DepositionMar 12, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionMar 28, 2018ID: 1KWN
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 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
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.530, 58.530, 151.350
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
DetailsThe biological assembly is a monomer (asymetric unit)

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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.: 230 / 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: 4

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Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.82 %
Crystal growTemperature: 293 K / Method: microdialysis / pH: 6.5
Details: Na-tartrate (0.52M), Na-ADA (0.1M), agarose gel (0.15% m/v). THE CRYSTALS WERE GROWN IN THE ADVANCED PROTEIN CRYSTALLIZATION FACILITY (APCF) ABOARD THE US SPACE SHUTTLE (MISSION STS-95) ...Details: Na-tartrate (0.52M), Na-ADA (0.1M), agarose gel (0.15% m/v). THE CRYSTALS WERE GROWN IN THE ADVANCED PROTEIN CRYSTALLIZATION FACILITY (APCF) ABOARD THE US SPACE SHUTTLE (MISSION STS-95) USING EITHER A DIALYSIS SETUP (3 CRYSTALS) OR A FREE-INTERFACE DIFFUSION SETUP (1 CRYSTAL)., pH 6.5, Dialysis in APCF reactor, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8337 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 10, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8337 Å / Relative weight: 1
ReflectionResolution: 1.2→20 Å / Num. obs: 82240 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 14.3 Å2 / Rmerge(I) obs: 0.036 / Rsym value: 0.036 / Net I/σ(I): 26.5
Reflection shellResolution: 1.2→1.23 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 2.05 / Num. unique obs: 5579 / Rsym value: 0.522 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1THW

1thw


Resolution: 1.2→19.96 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.988 / SU B: 0.79 / SU ML: 0.015 / SU R Cruickshank DPI: 0.0219 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.022 / ESU R Free: 0.022
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1171 4130 5 %RANDOM
Rwork0.103 ---
obs0.1037 78110 98.96 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 161.72 Å2 / Biso mean: 22.388 Å2 / Biso min: 10.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å2-0 Å2-0 Å2
2--0.31 Å2-0 Å2
3----0.62 Å2
Refinement stepCycle: final / Resolution: 1.2→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1539 0 10 235 1784
Biso mean--18.41 37.35 -
Num. residues----206
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021667
X-RAY DIFFRACTIONr_bond_other_d0.0020.021476
X-RAY DIFFRACTIONr_angle_refined_deg1.51.9542275
X-RAY DIFFRACTIONr_angle_other_deg0.95133450
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.595214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.5982370
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.01615261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.161513
X-RAY DIFFRACTIONr_chiral_restr0.0990.2249
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211877
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02360
X-RAY DIFFRACTIONr_rigid_bond_restr5.52531667
X-RAY DIFFRACTIONr_sphericity_free18.3220.01176
X-RAY DIFFRACTIONr_sphericity_bonded18.0560.011676
LS refinement shellResolution: 1.2→1.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 308 -
Rwork0.242 5579 -
all-5887 -
obs--97.86 %

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