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- PDB-5lh0: Low dose Thaumatin - 0-40 ms. -

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Basic information

Entry
Database: PDB / ID: 5lh0
TitleLow dose Thaumatin - 0-40 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 / molecular replacement / Resolution: 1.88 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-1 kcal/mol
Surface area9620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.440, 58.440, 151.580
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 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.: 51 / 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: 2.91 Å3/Da / Density % sol: 57.75 %
Crystal growTemperature: 296 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: 1.88→30 Å / Num. obs: 20283 / % possible obs: 92.6 % / Redundancy: 3.15 % / Rmerge(I) obs: 0.152 / Net I/σ(I): 5.3
Reflection shellResolution: 1.88→1.95 Å / Rmerge(I) obs: 0.525

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEVERSION November 3, 2014data scaling
MOLREPphasing
REFMAC5.8.0131refinement
PDB_EXTRACT3.2data extraction
MxCuBEdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LR2

1lr2


Resolution: 1.88→19.93 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.331 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.13 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2386 459 2.2 %RANDOM
Rwork0.1881 ---
obs0.1891 20283 93.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 111.25 Å2 / Biso mean: 22.643 Å2 / Biso min: 11.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 1.88→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1550 0 10 51 1611
Biso mean--20.38 23.17 -
Num. residues----207
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.021603
X-RAY DIFFRACTIONr_angle_refined_deg2.041.9522177
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0695206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.78523.0366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.1615241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7931512
X-RAY DIFFRACTIONr_chiral_restr0.1390.2232
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211235
X-RAY DIFFRACTIONr_mcbond_it2.2332.013827
X-RAY DIFFRACTIONr_mcangle_it3.3012.9981032
X-RAY DIFFRACTIONr_scbond_it4.2822.417776
LS refinement shellResolution: 1.88→1.928 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 36 -
Rwork0.254 1441 -
all-1477 -
obs--94.26 %

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