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- PDB-9fx4: Crystal structure of Cryo2RT Thaumatin at 100K -

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Basic information

Entry
Database: PDB / ID: 9fx4
TitleCrystal structure of Cryo2RT Thaumatin at 100K
ComponentsThaumatin I
KeywordsPLANT PROTEIN / cryo2RT / synchrotron / room-temperature / protein
Function / homology
Function and homology information


defense response / cytoplasmic vesicle / extracellular region
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
L(+)-TARTARIC ACID / Thaumatin I
Similarity search - Component
Biological speciesThaumatococcus daniellii (katemfe)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsHuang, C.Y. / Aumonier, S. / Olieric, V. / Wang, M.
Funding support Switzerland, European Union, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation182369 Switzerland
H2020 Marie Curie Actions of the European Commission884104 PSI-FELLOW-III-3iEuropean Union
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2024
Title: Cryo2RT: a high-throughput method for room-temperature macromolecular crystallography from cryo-cooled crystals.
Authors: Huang, C.Y. / Aumonier, S. / Olieric, V. / Wang, M.
History
DepositionJul 1, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2024Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 14, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Oct 16, 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

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Assembly

Deposited unit
A: Thaumatin I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6142
Polymers25,4641
Non-polymers1501
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint1 kcal/mol
Surface area9530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.864, 57.864, 149.9
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Thaumatin I / Thaumatin-1


Mass: 25463.881 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.: 309 / 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: 2.91 Å3/Da / Density % sol: 57.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.6M Na. K. Tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.59→45.8 Å / Num. obs: 35191 / % possible obs: 100 % / Redundancy: 25.7 % / CC1/2: 1 / Rrim(I) all: 0.089 / Net I/σ(I): 23.32
Reflection shellResolution: 1.59→1.69 Å / Mean I/σ(I) obs: 1.31 / Num. unique obs: 5547 / Rrim(I) all: 2.221 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→45.8 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.943 / SU R Cruickshank DPI: 0.08 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.092 / SU Rfree Blow DPI: 0.086 / SU Rfree Cruickshank DPI: 0.078
RfactorNum. reflection% reflectionSelection details
Rfree0.2103 1760 -RANDOM
Rwork0.1906 ---
obs0.1916 35186 99.9 %-
Displacement parametersBiso mean: 33.78 Å2
Baniso -1Baniso -2Baniso -3
1--5.1705 Å20 Å20 Å2
2---5.1705 Å20 Å2
3---10.341 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.59→45.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1551 0 10 309 1870
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011663HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.052267HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d560SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes283HARMONIC5
X-RAY DIFFRACTIONt_it1663HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion225SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1881SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.56
X-RAY DIFFRACTIONt_other_torsion14.77
LS refinement shellResolution: 1.59→1.6 Å
RfactorNum. reflection% reflection
Rfree0.3505 35 -
Rwork0.4038 --
obs0.4007 704 97.18 %

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