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- PDB-4ela: Final Thaumatin Structure for Radiation Damage Experiment at 300 K -

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Basic information

Entry
Database: PDB / ID: 4ela
TitleFinal Thaumatin Structure for Radiation Damage Experiment at 300 K
ComponentsThaumatin-1
KeywordsPLANT PROTEIN / sweet protein / radiation damage
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: 2 Å
AuthorsWarkentin, M. / Badeau, R. / Hopkins, J.B. / Thorne, R.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Spatial distribution of radiation damage to crystalline proteins at 25-300 K.
Authors: Warkentin, M. / Badeau, R. / Hopkins, J.B. / Thorne, R.E.
History
DepositionApr 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_entry_details.has_protein_modification / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.330, 58.330, 151.300
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: 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.: 131 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHAUMATIN WAS PURCHASED FROM SIGMA-ALDRICH (CATALOG # T7638) AND CONTAINED A MIXTURE OF THAUMATIN I ...THAUMATIN WAS PURCHASED FROM SIGMA-ALDRICH (CATALOG # T7638) AND CONTAINED A MIXTURE OF THAUMATIN I AND THAUMATIN II. LYS46 WAS USED IN PLACE OF ASN46 AND ASP113 WAS USED IN PLACE OF ASN113 AS WAS DONE IN ENTRY 1RQW AND AS SUGGESTED BY KO ET AL., ACTA CRYST. D50,813(1994).

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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: 2.89 Å3/Da / Density % sol: 57.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: sodium potassium tartrate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.917 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 22, 2010
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 1.52→99 Å / Num. obs: 17277 / % possible obs: 86.1 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.082 / Χ2: 0.856 / Net I/σ(I): 6.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.52-1.572.20.33110720.59126.4
1.57-1.6430.35120340.619150.5
1.64-1.7140.3833910.629183.6
1.71-1.860.34540080.616198.9
1.8-1.927.10.25540580.691199.7
1.92-2.067.20.16440860.764199.9
2.06-2.277.10.11741050.847199.9
2.27-2.67.10.0941360.853199.9
2.6-3.2870.06442110.937199.9
3.28-996.50.05544401.396199.2

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
BUSTER-TNTrefinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
DENZOdata reduction
BUSTER2.8.0phasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→46.19 Å / Cor.coef. Fo:Fc: 0.9564 / Cor.coef. Fo:Fc free: 0.9459 / Occupancy max: 1 / Occupancy min: 0.11 / SU R Cruickshank DPI: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1925 1025 5.93 %RANDOM
Rwork0.1607 ---
obs0.1625 17277 --
Displacement parametersBiso max: 129.47 Å2 / Biso mean: 31.9469 Å2 / Biso min: 14.5 Å2
Baniso -1Baniso -2Baniso -3
1--3.3496 Å20 Å20 Å2
2---3.3496 Å20 Å2
3---6.6991 Å2
Refine analyzeLuzzati coordinate error obs: 0.189 Å
Refinement stepCycle: LAST / Resolution: 2→46.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1552 0 10 131 1693
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d557SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes37HARMONIC2
X-RAY DIFFRACTIONt_gen_planes243HARMONIC5
X-RAY DIFFRACTIONt_it1664HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion225SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1911SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1664HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2265HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion4.07
X-RAY DIFFRACTIONt_other_torsion17.17
LS refinement shellResolution: 2→2.12 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2375 128 6.57 %
Rwork0.1942 1821 -
all0.1969 1949 -

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