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- PDB-8ena: Thaumatin native-SAD structure determined at 5 keV with a helium ... -

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Basic information

Entry
Database: PDB / ID: 8ena
TitleThaumatin native-SAD structure determined at 5 keV with a helium environmet
ComponentsThaumatin-1
KeywordsPLANT PROTEIN / anomalous diffration / native SAD / low energy / helium path
Function / homologyThaumatin, conserved site / Thaumatin family signature. / Thaumatin family / Thaumatin family / Thaumatin family profile. / Thaumatin family / Osmotin/thaumatin-like superfamily / cytoplasmic vesicle / Thaumatin I
Function and homology information
Biological speciesThaumatococcus daniellii (katemfe)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsKarasawa, A. / Andi, B. / Ruchs, M.R. / Shi, W. / McSweeney, S. / Hendrickson, W.A. / Liu, Q.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116799 United States
CitationJournal: Iucrj / Year: 2022
Title: Multi-crystal native-SAD phasing at 5 keV with a helium environment.
Authors: Karasawa, A. / Andi, B. / Fuchs, M.R. / Shi, W. / McSweeney, S. / Hendrickson, W.A. / Liu, Q.
History
DepositionSep 29, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2022Group: Database references / Category: citation / Item: _citation.page_first / _citation.page_last
Revision 1.2May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 20, 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


Theoretical massNumber of molelcules
Total (without water)22,2271
Polymers22,2271
Non-polymers00
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.642, 57.642, 150.233
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 56.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.7 M sodium tartrate, 100 mM ADA, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 2.479 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.479 Å / Relative weight: 1
ReflectionResolution: 2.5→39.34 Å / Num. obs: 16225 / % possible obs: 97.1 % / Redundancy: 183.6 % / Biso Wilson estimate: 27.96 Å2 / CC1/2: 0.979 / Net I/σ(I): 20
Reflection shellResolution: 2.5→2.53 Å / Num. unique obs: 372 / CC1/2: 0.065

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Processing

Software
NameVersionClassification
PHENIX1.18.2-3874refinement
DIALSv1-1545data reduction
Aimless0.5.17data scaling
PHASER2.5.7phasing
BUCCANEERmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.5→39.34 Å / SU ML: 0.3944 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.3247
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2336 876 5.42 %
Rwork0.1854 15276 -
obs0.1879 16152 96.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.16 Å2
Refinement stepCycle: LAST / Resolution: 2.5→39.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1550 0 0 118 1668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00461586
X-RAY DIFFRACTIONf_angle_d0.79512150
X-RAY DIFFRACTIONf_chiral_restr0.047230
X-RAY DIFFRACTIONf_plane_restr0.0051284
X-RAY DIFFRACTIONf_dihedral_angle_d5.9032226
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.660.62261120.46082089X-RAY DIFFRACTION79.83
2.66-2.860.32041650.2662640X-RAY DIFFRACTION99.96
2.86-3.150.26031380.19812659X-RAY DIFFRACTION100
3.15-3.610.20211390.15962639X-RAY DIFFRACTION100
3.61-4.540.16961650.13072609X-RAY DIFFRACTION99.96
4.54-39.340.18061570.15372640X-RAY DIFFRACTION99.96

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