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- PDB-9fx5: Crystal structure of Cryo2RT Thaumatin at 296K -

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Basic information

Entry
Database: PDB / ID: 9fx5
TitleCrystal structure of Cryo2RT Thaumatin at 296K
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: 1.592 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

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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
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint1 kcal/mol
Surface area9720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.449, 58.449, 151.499
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.: 219 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 296 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→46.28 Å / Num. obs: 36150 / % possible obs: 100 % / Redundancy: 26.15 % / CC1/2: 1 / Rrim(I) all: 0.07 / Net I/σ(I): 27.46
Reflection shellResolution: 1.59→1.69 Å / Redundancy: 26.67 % / Mean I/σ(I) obs: 1.15 / Num. unique obs: 5700 / CC1/2: 0.74 / Rrim(I) all: 2.31 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IN HOUSE MODEL

Resolution: 1.592→46.27 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU R Cruickshank DPI: 0.077 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.085 / SU Rfree Blow DPI: 0.085 / SU Rfree Cruickshank DPI: 0.079
RfactorNum. reflection% reflectionSelection details
Rfree0.2212 1798 -RANDOM
Rwork0.193 ---
obs0.1944 35978 99.6 %-
Displacement parametersBiso mean: 32.95 Å2
Baniso -1Baniso -2Baniso -3
1--1.9033 Å20 Å20 Å2
2---1.9033 Å20 Å2
3---3.8066 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.592→46.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1551 0 10 219 1780
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011662HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.042264HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d561SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes282HARMONIC5
X-RAY DIFFRACTIONt_it1662HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion224SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1532SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.43
X-RAY DIFFRACTIONt_other_torsion14.82
LS refinement shellResolution: 1.592→1.61 Å
RfactorNum. reflection% reflection
Rfree0.841 35 -
Rwork0.7156 --
obs--83.03 %

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