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- PDB-5kvw: T. danielli thaumatin at 100K, Data set 1 -

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Basic information

Entry
Database: PDB / ID: 5kvw
TitleT. danielli thaumatin at 100K, Data set 1
ComponentsThaumatin-1
KeywordsPLANT PROTEIN / Conformational variation / Radiation damage
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: 1.59 Å
AuthorsRussi, S. / Gonzalez, A. / Kenner, L.R. / Keedy, D.A. / Fraser, J.S. / van den Bedem, H.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103393 United States
Department of Energy (DOE, United States)DE-AC02-76SF00515 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110580 United States
National Science Foundation (NSF, United States)STC-1231306 United States
CitationJournal: J Synchrotron Radiat / Year: 2017
Title: Conformational variation of proteins at room temperature is not dominated by radiation damage.
Authors: Russi, S. / Gonzalez, A. / Kenner, L.R. / Keedy, D.A. / Fraser, J.S. / van den Bedem, H.
History
DepositionJul 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 16, 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)22,6535
Polymers22,2271
Non-polymers4264
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.469, 57.469, 150.933
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: 22227.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thaumatococcus daniellii (katemfe) / Production host: 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.8 Å3/Da / Density % sol: 56.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: CRYSTALS WERE GROWN BY MIXING EQUAL VOLUMES OF WELL SOLUTION (0.9 M SODIUM/POTASSIUM TARTRATE, 0.2 M AMMONIUM SULFATE, 15% GLYCEROL, 25% PEG 8000, 100 MM HEPES PH 7.3) AND PROTEIN (35 MG/ML) ...Details: CRYSTALS WERE GROWN BY MIXING EQUAL VOLUMES OF WELL SOLUTION (0.9 M SODIUM/POTASSIUM TARTRATE, 0.2 M AMMONIUM SULFATE, 15% GLYCEROL, 25% PEG 8000, 100 MM HEPES PH 7.3) AND PROTEIN (35 MG/ML) IN THE SITTING DROP FORMAT.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.21549 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.21549 Å / Relative weight: 1
ReflectionResolution: 1.59→31.613 Å / Num. all: 34655 / Num. obs: 34655 / % possible obs: 99 % / Redundancy: 4.1 % / Rpim(I) all: 0.024 / Rrim(I) all: 0.05 / Rsym value: 0.044 / Net I/av σ(I): 10.091 / Net I/σ(I): 15.1 / Num. measured all: 141558
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.59-1.683.40.7281.11607247670.4520.8630.7281.695.3
1.68-1.784.20.4871.62010647460.2680.5570.4872.9100
1.78-1.94.30.2782.81912444800.1520.3180.2784.899.9
1.9-2.054.30.1495.21783741810.0810.170.1498.599.9
2.05-2.254.30.0868.81643938610.0470.0980.08613.699.9
2.25-2.514.20.05912.41475735080.0330.0680.0591999.8
2.51-2.94.20.04316.11302731170.0240.050.04325.899.5
2.9-3.564.10.03119.71100926570.0170.0360.03137.199.4
3.56-5.034.10.02522852120960.0140.0290.0254599
5.03-31.6133.80.02321466612420.0140.0270.02340.898.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
XDSdata reduction
SCALA3.3.20data scaling
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RQW

1rqw


Resolution: 1.59→31.61 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.358 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1956 1733 5 %RANDOM
Rwork0.1622 ---
obs0.164 32840 98.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.94 Å2 / Biso mean: 26.895 Å2 / Biso min: 14.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å2-0 Å2-0 Å2
2--0.95 Å20 Å2
3----1.91 Å2
Refinement stepCycle: final / Resolution: 1.59→31.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1551 0 28 147 1726
Biso mean--36.87 39.63 -
Num. residues----207
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0192485
X-RAY DIFFRACTIONr_bond_other_d0.0030.022219
X-RAY DIFFRACTIONr_angle_refined_deg2.151.963462
X-RAY DIFFRACTIONr_angle_other_deg1.1553.0085152
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.755.099355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.60322.92999
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.99515371
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0741519
X-RAY DIFFRACTIONr_chiral_restr0.1240.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213079
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02600
X-RAY DIFFRACTIONr_mcbond_it2.2662.5221273
X-RAY DIFFRACTIONr_mcbond_other2.2542.5171272
X-RAY DIFFRACTIONr_mcangle_it3.2063.7731670
LS refinement shellResolution: 1.59→1.631 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 115 -
Rwork0.323 2199 -
all-2314 -
obs--90.82 %

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