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- PDB-2blu: Thaumatin After A High Dose X-Ray "Burn" -

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Basic information

Entry
Database: PDB / ID: 2blu
TitleThaumatin After A High Dose X-Ray "Burn"
ComponentsTHAUMATIN I
KeywordsPLANT PROTEIN / RADIATION DAMAGE / SYNCHROTRON / PHASING / RIP / TASTE-MODIFYING 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 / OTHER / Resolution: 1.4 Å
AuthorsNanao, M.H. / Ravelli, R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Improving Radiation-Damage Substructures for Rip.
Authors: Nanao, M.H. / Sheldrick, G.M. / Ravelli, R.B.
History
DepositionMar 8, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2005Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Source and taxonomy / Version format compliance
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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)22,3062
Polymers22,1561
Non-polymers1501
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)57.780, 57.780, 150.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein THAUMATIN I


Mass: 22155.980 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-206 / 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.: 276 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTASTE-MODIFYING PROTEIN; INTENSELY SWEET-TASTING. IT IS 100000 TIMES SWEETER THAN SUCROSE ON A MOLAR BASIS.
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: 2.83 Å3/Da / Density % sol: 56.2 %
Crystal growDetails: 0.9 M SODIUM/POTASSIUM TARTRATE, 0.1 M HEPES, PH 7.3, 15 % GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9392
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 18, 2004 / Details: BENT MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9392 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 93941 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 15.38
Reflection shellResolution: 1.4→1.49 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.35 / % possible all: 97.2

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
SHELXEphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: OTHER / Resolution: 1.4→45 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.264 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.155 2538 5.1 %RANDOM
Rwork0.125 ---
obs0.127 47378 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 9.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20 Å2
2--0.19 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.4→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1546 0 10 276 1832
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221666
X-RAY DIFFRACTIONr_bond_other_d0.0010.021413
X-RAY DIFFRACTIONr_angle_refined_deg1.6521.9572277
X-RAY DIFFRACTIONr_angle_other_deg0.85633313
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8275221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.34923.42970
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.90915253
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5241512
X-RAY DIFFRACTIONr_chiral_restr0.1070.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021939
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02358
X-RAY DIFFRACTIONr_nbd_refined0.2090.2302
X-RAY DIFFRACTIONr_nbd_other0.1920.21407
X-RAY DIFFRACTIONr_nbtor_refined0.1840.2835
X-RAY DIFFRACTIONr_nbtor_other0.0850.2934
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.2170
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.130.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2840.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9371.51353
X-RAY DIFFRACTIONr_mcbond_other0.791.5441
X-RAY DIFFRACTIONr_mcangle_it2.37921717
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5033717
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.3954.5559
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.68933756
X-RAY DIFFRACTIONr_sphericity_free10.8163276
X-RAY DIFFRACTIONr_sphericity_bonded3.70333027
LS refinement shellResolution: 1.4→1.48 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.196 370 -
Rwork0.151 6647 -
obs--96.19 %

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