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- PDB-3dzr: Thaumatin by Classical hanging drop method before high X-Ray dose... -

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Basic information

Entry
Database: PDB / ID: 3dzr
TitleThaumatin by Classical hanging drop method before high X-Ray dose on ESRF ID29 beamline
ComponentsThaumatin-1
KeywordsPLANT PROTEIN
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: 1.51 Å
AuthorsTripathi, S. / Pechkova, E. / Nicolini, C.
CitationJournal: To be Published
Title: Radiation damage in protein structural characterization by Synchrotron Radiation: State of the art and Nanotechnology-based perspective
Authors: Pechkova, E. / Tripathi, S. / Nicolini, C.
History
DepositionJul 30, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 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)22,3932
Polymers22,2431
Non-polymers1501
Water7,170398
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.814, 57.814, 150.196
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1282-

HOH

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Components

#1: Protein Thaumatin-1


Mass: 22243.119 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.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 56.4 % / Mosaicity: 0.33 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM ADA, 1M Na/K-tartrate, 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: 0.9787 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 29, 2007 / Details: toroidal mirror
RadiationMonochromator: Si 311 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.51→53.955 Å / Num. obs: 41007 / % possible obs: 100 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.077 / Rsym value: 0.077
Reflection shellResolution: 1.51→1.59 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.105 / Mean I/σ(I) obs: 6.2 / Num. measured all: 45471 / Num. unique all: 5857 / Rsym value: 0.105 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RQW

1rqw


Resolution: 1.51→45.83 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.963 / Occupancy max: 1 / Occupancy min: 0.11 / FOM work R set: 0.926 / SU B: 1.481 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.153 2056 5 %RANDOM
Rwork0.137 ---
obs0.138 40938 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 148.79 Å2 / Biso mean: 16.559 Å2 / Biso min: 4.89 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.51→45.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1604 0 10 398 2012
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0221664
X-RAY DIFFRACTIONr_angle_refined_deg1.1051.9622265
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1325208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.99123.18869
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.81615268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3431512
X-RAY DIFFRACTIONr_chiral_restr0.0760.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021263
X-RAY DIFFRACTIONr_nbd_refined0.2040.3790
X-RAY DIFFRACTIONr_nbtor_refined0.3150.51162
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.5528
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.359
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.575
X-RAY DIFFRACTIONr_mcbond_it1.41221063
X-RAY DIFFRACTIONr_mcangle_it2.32931683
X-RAY DIFFRACTIONr_scbond_it1.5182685
X-RAY DIFFRACTIONr_scangle_it2.4933582
LS refinement shellResolution: 1.51→1.549 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.149 176 -
Rwork0.113 2791 -
all-2967 -
obs--100 %

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