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- PDB-3v84: Thaumatin by LB based Hanging Drop Vapour Diffusion after 1.81 MG... -

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Basic information

Entry
Database: PDB / ID: 3v84
TitleThaumatin by LB based Hanging Drop Vapour Diffusion after 1.81 MGy X-Ray dose at ESRF ID29 beamline (Worst Case)
ComponentsThaumatin I
KeywordsPLANT PROTEIN / radiation damage / thin film / Langmuir-Blodgett / LB
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
Thaumatin I / Thaumatin I
Similarity search - Component
Biological speciesThaumatococcus daniellii (katemfe)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsBelmonte, L. / Scudieri, D. / Tripathi, S. / Pechkova, E. / Nicolini, C.
CitationJournal: CRIT.REV.EUKARYOT.GENE EXPR. / Year: 2012
Title: Langmuir-Blodgett nanotemplate and radiation resistance in protein crystals: state of the art.
Authors: Belmonte, L. / Pechkova, E. / Tripathi, S. / Scudieri, D. / Nicolini, C.
History
DepositionDec 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 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 I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5965
Polymers22,2281
Non-polymers3684
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.776, 57.776, 150.111
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-523-

HOH

21A-592-

HOH

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Components

#1: Protein Thaumatin I


Mass: 22228.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thaumatococcus daniellii (katemfe) / References: UniProt: Q8RVT0, UniProt: P02883*PLUS
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.82 Å3/Da / Density % sol: 56.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 6 uL protein solution containing 18 mg/mL thaumatin in 100 mM ADA disodium salt buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97633 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 10, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97633 Å / Relative weight: 1
ReflectionResolution: 1.5→45.783 Å / Num. all: 11979 / Num. obs: 11936 / % possible obs: 99.2 % / Redundancy: 14.1 % / Rsym value: 0.047 / Net I/σ(I): 41.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.5-1.5814.70.0997.40.099198.4
1.58-1.6813.90.0890.08198.7
1.68-1.7914.90.06610.50.066198.9
1.79-1.9414.60.05611.90.056199.1
1.94-2.1213.50.04813.10.048199.4
2.12-2.3714.70.04414.20.044199.6
2.37-2.7414.10.04214.50.042199.7
2.74-3.3513.10.0413.90.04199.9
3.35-4.7413.50.04312.90.043199.9
4.74-45.78311.90.045120.045199.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.61 Å45.78 Å
Translation1.61 Å45.78 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
PXSOFTdata collection
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ALD

3ald


Resolution: 2.3→45.78 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.864 / Occupancy max: 1 / Occupancy min: 1 / SU B: 5.793 / SU ML: 0.142 / SU R Cruickshank DPI: 0.0652 / Cross valid method: THROUGHOUT / ESU R: 0.275 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23775 570 4.8 %RANDOM
Rwork0.18192 ---
obs0.18466 11360 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 6.841 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2--0.16 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 2.3→45.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1551 0 24 198 1773
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221615
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8511.9612188
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8915206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.22923.0366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.59815241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0861512
X-RAY DIFFRACTIONr_chiral_restr0.1140.2230
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211235
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.7641.51023
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.48721641
X-RAY DIFFRACTIONr_scbond_it2.8273592
X-RAY DIFFRACTIONr_scangle_it4.7184.5547
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 32 -
Rwork0.182 813 -
obs--99.18 %

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