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- PDB-4diy: Thaumatin I by Classical Hanging Drop Method at 1.98A resolution ... -

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Basic information

Entry
Database: PDB / ID: 4diy
TitleThaumatin I by Classical Hanging Drop Method at 1.98A resolution for Unique Water Distribution
ComponentsThaumatin I
KeywordsPLANT PROTEIN / Water Distribution / Thin-Film / Langmuir-Blodgett
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: 1.98 Å
AuthorsPechkova, E. / Sivozhelezov, V. / Belmonte, L. / Nicolini, C.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: Unique water distribution of Langmuir-Blodgett versus classical crystals.
Authors: Pechkova, E. / Sivozhelezov, V. / Belmonte, L. / Nicolini, C.
History
DepositionFeb 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Nov 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thaumatin I


Theoretical massNumber of molelcules
Total (without water)22,2431
Polymers22,2431
Non-polymers00
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.710, 57.710, 149.950
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 I


Mass: 22243.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thaumatococcus daniellii (katemfe) / References: UniProt: Q8RVT0, UniProt: P02883*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.81 Å3/Da / Density % sol: 56.17 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97633 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97633 Å / Relative weight: 1
ReflectionResolution: 1.98→53.86 Å / Num. all: 18511 / Num. obs: 18511 / % possible obs: 100 % / Redundancy: 13.6 % / Rsym value: 0.065 / Net I/σ(I): 33.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.98-2.0913.80.1175.83634326290.117100
2.09-2.2114.10.0887.63497124860.088100
2.21-2.37140.0719.63276023400.071100
2.37-2.5613.90.06410.23079622160.064100
2.56-2.813.80.0659.82831920480.065100
2.8-3.1313.60.0512.32529218550.05100
3.13-3.6113.40.0511.32219416600.05100
3.61-4.43130.0727.61857914340.072100
4.43-6.2611.90.0677.41358811430.067100
6.26-53.85911.80.041282377000.0499.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.05 Å53.86 Å
Translation2.05 Å53.86 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→53.86 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.2113 / WRfactor Rwork: 0.1853 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.881 / SU B: 2.69 / SU ML: 0.077 / SU R Cruickshank DPI: 0.1408 / SU Rfree: 0.1284 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2014 943 5.1 %RANDOM
Rwork0.1711 ---
obs0.1726 18432 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 59.69 Å2 / Biso mean: 12.4728 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20 Å2
2--0.21 Å20 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.98→53.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1552 0 0 197 1749
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0221596
X-RAY DIFFRACTIONr_angle_refined_deg1.981.9532168
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6465206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.8722.92365
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.7715244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0361512
X-RAY DIFFRACTIONr_chiral_restr0.1670.2230
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211231
X-RAY DIFFRACTIONr_mcbond_it1.2951.51023
X-RAY DIFFRACTIONr_mcangle_it2.17421641
X-RAY DIFFRACTIONr_scbond_it3.5913573
X-RAY DIFFRACTIONr_scangle_it5.8214.5527
LS refinement shellResolution: 1.98→2.032 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.184 64 -
Rwork0.179 1244 -
all-1308 -
obs--99.92 %

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