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- PDB-5lmh: High dose Thaumatin - 160-200 ms. -

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Basic information

Entry
Database: PDB / ID: 5lmh
TitleHigh dose Thaumatin - 160-200 ms.
ComponentsThaumatin-1
KeywordsPLANT PROTEIN / Multicrystal / Room-Temperature / Thaumatin
Function / homology
Function and homology information


defense response / cytoplasmic vesicle / extracellular region
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: 1.96 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 30, 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 2.0Dec 19, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_nonpoly_scheme ...atom_site / pdbx_nonpoly_scheme / pdbx_validate_symm_contact / struct_conn / struct_conn_type
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_nonpoly_scheme.auth_seq_num
Revision 2.1Jan 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 2.2Oct 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)22,5273
Polymers22,2271
Non-polymers3002
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-1 kcal/mol
Surface area10050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.480, 58.480, 151.730
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


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


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.92 Å3/Da / Density % sol: 57.85 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: .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: 1.96→19.95 Å / Num. obs: 18364 / % possible obs: 93.1 % / Redundancy: 3.2 % / CC1/2: 0.986 / Rmerge(I) obs: 0.143 / Net I/σ(I): 5.8
Reflection shellResolution: 1.96→2.03 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.663 / Mean I/σ(I) obs: 1.9 / CC1/2: 0.65 / % possible all: 93.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LR2

1lr2


Resolution: 1.96→19.95 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.915 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.14 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.223 923 5 %RANDOM
Rwork0.1786 ---
obs0.1808 17418 92.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 105.19 Å2 / Biso mean: 30.245 Å2 / Biso min: 16.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å2-0 Å2
2--0.03 Å2-0 Å2
3----0.07 Å2
Refinement stepCycle: final / Resolution: 1.96→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1550 0 20 71 1641
Biso mean--50.89 35.83 -
Num. residues----207
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021612
X-RAY DIFFRACTIONr_angle_refined_deg1.6911.9582189
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8425206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.5423.0366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.76715241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3081512
X-RAY DIFFRACTIONr_chiral_restr0.1210.2234
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211243
X-RAY DIFFRACTIONr_mcbond_it2.2012.756827
X-RAY DIFFRACTIONr_mcangle_it3.3934.1151032
X-RAY DIFFRACTIONr_scbond_it3.7393.153785
LS refinement shellResolution: 1.96→2.01 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 82 -
Rwork0.266 1238 -
all-1320 -
obs--93.22 %

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