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- PDB-6rvo: Multicrystal dataset of thaumatin collected using a multilayer mo... -

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Basic information

Entry
Database: PDB / ID: 6rvo
TitleMulticrystal dataset of thaumatin collected using a multilayer monochromator.
ComponentsThaumatin I
KeywordsPLANT PROTEIN / multilayer multicrystal VMXi
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: 1.97 Å
AuthorsSandy, J. / Sanchez-Weatherby, J. / Mikolajek, H. / Winter, G.
CitationJournal: Iucrj / Year: 2023
Title: Protein-to-structure pipeline for ambient-temperature crystallography at VMXi
Authors: Mikolajek, H. / Sanchez-Weatherby, J. / Sandy, J. / Gildea, R.G. / Campeotto, I. / Cheruvara, H. / Clarke, J.D. / Foster, T. / Fujii, S. / Paulsen, I.T. / Shah, B.S. / Hough, M.A.
History
DepositionMay 31, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Category: diffrn_detector / diffrn_source
Item: _diffrn_detector.type / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.2May 17, 2023Group: Database references / Refinement description
Category: citation / citation_author ...citation / citation_author / database_2 / refine
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)22,3782
Polymers22,2281
Non-polymers1501
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30 Å2
ΔGint-0 kcal/mol
Surface area9610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.563, 58.563, 151.496
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 / / Thaumatin-1


Mass: 22228.043 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 / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 16

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Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.9 %
Crystal growTemperature: 293 K / Method: counter-diffusion / pH: 5.6 / Details: 0.1 M Sodium citrate pH 5.6 0.75M Na/K Tartrate

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: VMXi / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: May 22, 2019 / Details: Multilayer monochromator
RadiationMonochromator: Multilayer monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.97→58.56 Å / Num. obs: 19537 / % possible obs: 99.98 % / Redundancy: 38.7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.409 / Rpim(I) all: 0.062 / Rrim(I) all: 0.414 / Net I/σ(I): 8.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.97-28.62.1790.79500.3890.782.32399.79
5.35-58.5649.60.21521.911330.9940.030.21799.91

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RQW

1rqw


Resolution: 1.97→54.624 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1762 1941 9.98 %Random selection
Rwork0.1417 ---
obs0.1451 19444 99.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.97→54.624 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1540 0 10 143 1693
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011609
X-RAY DIFFRACTIONf_angle_d0.8662194
X-RAY DIFFRACTIONf_dihedral_angle_d2.9741279
X-RAY DIFFRACTIONf_chiral_restr0.053235
X-RAY DIFFRACTIONf_plane_restr0.006289
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9701-2.01930.3151330.2941219X-RAY DIFFRACTION98
2.0193-2.07390.26441320.24731202X-RAY DIFFRACTION100
2.0739-2.1350.21121350.19771217X-RAY DIFFRACTION100
2.135-2.20390.2111360.17091221X-RAY DIFFRACTION100
2.2039-2.28270.20461360.14821224X-RAY DIFFRACTION100
2.2827-2.3740.20291370.14291240X-RAY DIFFRACTION100
2.374-2.48210.17471370.13121227X-RAY DIFFRACTION100
2.4821-2.6130.19011380.13371241X-RAY DIFFRACTION100
2.613-2.77670.1741390.14831250X-RAY DIFFRACTION100
2.7767-2.9910.17961380.14961242X-RAY DIFFRACTION100
2.991-3.2920.19051400.14551258X-RAY DIFFRACTION100
3.292-3.76830.16951410.12031274X-RAY DIFFRACTION100
3.7683-4.74720.12361430.09561288X-RAY DIFFRACTION100
4.7472-54.64470.1411560.13191400X-RAY DIFFRACTION100

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