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- PDB-7ac3: Structure of thaumatin collected by rotation serial crystallograp... -

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Basic information

Entry
Database: PDB / ID: 7ac3
TitleStructure of thaumatin collected by rotation serial crystallography on a COC membrane at a synchrotron source
ComponentsThaumatin-1
KeywordsPLANT PROTEIN
Function / homology
Function and homology information


cytoplasmic vesicle
Similarity search - Function
Thaumatin, conserved site / Thaumatin family signature. / Thaumatin family / Thaumatin family / Thaumatin family profile. / Thaumatin family / Osmotin/thaumatin-like superfamily
Similarity search - Domain/homology
S-1,2-PROPANEDIOL / L(+)-TARTARIC ACID / Thaumatin I
Similarity search - Component
Biological speciesThaumatococcus daniellii (katemfe)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsMartiel, I. / Padeste, C. / Karpik, A. / Huang, C.Y. / Vera, L. / Wang, M. / Marsh, M.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Versatile microporous polymer-based supports for serial macromolecular crystallography.
Authors: Martiel, I. / Beale, J.H. / Karpik, A. / Huang, C.Y. / Vera, L. / Olieric, N. / Wranik, M. / Tsai, C.J. / Muhle, J. / Aurelius, O. / John, J. / Hogbom, M. / Wang, M. / Marsh, M. / Padeste, C.
History
DepositionSep 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thaumatin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5756
Polymers22,2271
Non-polymers3485
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-12 kcal/mol
Surface area9340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.000, 58.000, 150.310
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: Escherichia coli (E. coli) / 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-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.84 Å3/Da / Density % sol: 56.75 %
Crystal growTemperature: 293 K / Method: batch mode
Details: 1.6 M potassium sodium tartrate tetrahydrate, 100mM Na Hepes pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→45.92 Å / Num. obs: 31814 / % possible obs: 99.5 % / Redundancy: 7.98 % / CC1/2: 0.986 / Net I/σ(I): 4.19
Reflection shellResolution: 1.65→1.69 Å / Mean I/σ(I) obs: 0.54 / Num. unique obs: 3127 / CC1/2: 0.144

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AXR

4axr


Resolution: 1.65→45.916 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2106 1591 5 %
Rwork0.1654 30223 -
obs0.1677 31814 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.35 Å2 / Biso mean: 26.2115 Å2 / Biso min: 14.42 Å2
Refinement stepCycle: final / Resolution: 1.65→45.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1526 0 22 291 1839
Biso mean--39.79 38.84 -
Num. residues----206
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.65-1.70330.39141410.33192680
1.7033-1.76410.31011410.28992691
1.7641-1.83480.27871420.24342686
1.8348-1.91830.26591420.21772707
1.9183-2.01940.24981420.19912700
2.0194-2.14590.23351440.17022722
2.1459-2.31160.18951430.15282729
2.3116-2.54420.19711450.15652748
2.5442-2.91240.24361460.16452771
2.9124-3.6690.19281480.14462810
3.669-45.9160.16621570.13512979
Refinement TLS params.Method: refined / Origin x: 4.6149 Å / Origin y: -16.6534 Å / Origin z: -4.8596 Å
111213212223313233
T0.1533 Å2-0.0083 Å20.0025 Å2-0.1381 Å2-0.0113 Å2--0.1649 Å2
L0.7989 °20.0959 °2-0.5696 °2-0.4639 °2-0.3054 °2--1.5193 °2
S0.0433 Å °-0.0381 Å °0.0466 Å °0.0089 Å °-0.0028 Å °-0.0032 Å °-0.0952 Å °0.0106 Å °-0.0315 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 206
2X-RAY DIFFRACTION1allA207 - 401
3X-RAY DIFFRACTION1allS1 - 296
4X-RAY DIFFRACTION1allB1 - 2

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