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- PDB-5lh7: High dose Thaumatin - 760-800 ms. -

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Basic information

Entry
Database: PDB / ID: 5lh7
TitleHigh dose Thaumatin - 760-800 ms.
ComponentsThaumatin-1
KeywordsPLANT PROTEIN / Multicrystal / Room-Temperature / Thaumatin
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: 2.28 Å
AuthorsSchubert, R. / Kapis, S. / Heymann, M. / Giquel, Y. / Bourenkov, G. / Schneider, T. / Betzel, C. / Perbandt, M.
CitationJournal: IUCrJ / Year: 2016
Title: A multicrystal diffraction data-collection approach for studying structural dynamics with millisecond temporal resolution.
Authors: Schubert, R. / Kapis, S. / Gicquel, Y. / Bourenkov, G. / Schneider, T.R. / Heymann, M. / Betzel, C. / Perbandt, M.
History
DepositionJul 8, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 10, 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

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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)22,5273
Polymers22,2271
Non-polymers3002
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint0 kcal/mol
Surface area9800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.450, 58.450, 151.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.91 Å3/Da / Density % sol: 57.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.3 M sodium tartrate and 50 mM Tris, pH 6.8

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Data collection

DiffractionMean temperature: 296 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.96863 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 2.28→30 Å / Num. obs: 11604 / % possible obs: 90.1 % / Redundancy: 3 % / Biso Wilson estimate: 39.589 Å2 / Rmerge(I) obs: 0.196 / Net I/σ(I): 5.9
Reflection shellResolution: 2.28→2.36 Å / Rmerge(I) obs: 0.835

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0131refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LR2

1lr2


Resolution: 2.28→19.94 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.934 / SU B: 6.361 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.227 / ESU R Free: 0.203 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2315 257 2.2 %RANDOM
Rwork0.1723 ---
obs0.1735 11604 90.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 209.17 Å2 / Biso mean: 31.766 Å2 / Biso min: 14.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å2-0 Å2
2--0.02 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 2.28→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1550 0 20 46 1616
Biso mean--115.74 34.26 -
Num. residues----207
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.021612
X-RAY DIFFRACTIONr_angle_refined_deg2.0711.9582189
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7715206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.71223.0366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.55315241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1091512
X-RAY DIFFRACTIONr_chiral_restr0.1190.2234
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211243
X-RAY DIFFRACTIONr_mcbond_it2.6132.846827
X-RAY DIFFRACTIONr_mcangle_it3.9444.2521032
X-RAY DIFFRACTIONr_scbond_it5.0333.378785
LS refinement shellResolution: 2.26→2.318 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 16 -
Rwork0.261 819 -
all-835 -
obs--91.16 %

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