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- PDB-9g2j: Thaumatin structure determined using SoS chip at ID29 (serial cry... -

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Basic information

Entry
Database: PDB / ID: 9g2j
TitleThaumatin structure determined using SoS chip at ID29 (serial crystallography)
ComponentsThaumatin I
KeywordsPLANT PROTEIN / Thaumatin
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
L(+)-TARTARIC ACID / Thaumatin I
Similarity search - Component
Biological speciesThaumatococcus daniellii (katemfe)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsDoak, R.B. / Shoeman, R.L. / Gorel, A. / Barends, T.R.M. / Schlichting, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: J.Appl.Crystallogr. / Year: 2024
Title: Sheet-on-sheet fixed target data collection devices for serial crystallography at synchrotron and XFEL sources.
Authors: Doak, R.B. / Shoeman, R.L. / Gorel, A. / Nizinski, S. / Barends, T.R.M. / Schlichting, I.
History
DepositionJul 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release

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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)22,3932
Polymers22,2431
Non-polymers1501
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint1 kcal/mol
Surface area9480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.849, 57.849, 150.328
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 I / Thaumatin-1


Mass: 22243.119 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.: 128 / 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: 2.83 Å3/Da / Density % sol: 56.49 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 7 / Details: 0.8 M NA, K TARTRATE, 0.1 M NA HEPES

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.073 Å
DetectorType: PSI JUNGFRAU 4M / Detector: PIXEL / Date: Jan 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.073 Å / Relative weight: 1
ReflectionResolution: 1.69→38 Å / Num. obs: 29237 / % possible obs: 100 % / Redundancy: 4475 % / R split: 0.067 / Net I/σ(I): 15.1
Reflection shellResolution: 1.69→1.8 Å / Num. unique obs: 1412 / R split: 0.73

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→37.904 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.657 / SU ML: 0.053 / Cross valid method: FREE R-VALUE / ESU R: 0.078 / ESU R Free: 0.072
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1688 1412 4.829 %
Rwork0.1576 27825 -
all0.158 --
obs-29237 98.934 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 28.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.389 Å20 Å2-0 Å2
2--0.389 Å2-0 Å2
3----0.777 Å2
Refinement stepCycle: LAST / Resolution: 1.69→37.904 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1546 0 10 128 1684
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0111629
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161460
X-RAY DIFFRACTIONr_angle_refined_deg1.7511.6562222
X-RAY DIFFRACTIONr_angle_other_deg0.641.5683388
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9465217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.124512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.89810251
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.5351067
X-RAY DIFFRACTIONr_chiral_restr0.0890.2238
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021960
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02392
X-RAY DIFFRACTIONr_nbd_refined0.210.2300
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.21442
X-RAY DIFFRACTIONr_nbtor_refined0.1940.2878
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0950.2982
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2380.298
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2140.215
X-RAY DIFFRACTIONr_nbd_other0.210.259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1970.220
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0280.22
X-RAY DIFFRACTIONr_mcbond_it2.4992.681835
X-RAY DIFFRACTIONr_mcbond_other2.4882.68835
X-RAY DIFFRACTIONr_mcangle_it3.3854.7861045
X-RAY DIFFRACTIONr_mcangle_other3.3884.7881046
X-RAY DIFFRACTIONr_scbond_it4.9223.242794
X-RAY DIFFRACTIONr_scbond_other4.9243.241793
X-RAY DIFFRACTIONr_scangle_it7.4385.6321171
X-RAY DIFFRACTIONr_scangle_other7.4395.6311171
X-RAY DIFFRACTIONr_lrange_it8.55828.6581877
X-RAY DIFFRACTIONr_lrange_other8.52328.3071862
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.69-1.7330.237680.2819280.27821390.9530.94493.31460.259
1.733-1.7810.2461160.23119600.23220760.9540.9641000.204
1.781-1.8320.213970.219290.220260.9710.9741000.168
1.832-1.8890.1971060.17718480.17819540.9750.981000.144
1.889-1.950.181900.15118390.15319290.980.9861000.124
1.95-2.0190.133820.13617660.13518480.990.9891000.114
2.019-2.0950.145830.13617160.13717990.9870.9881000.113
2.095-2.180.171830.16714700.16717210.9580.9790.23820.142
2.18-2.2760.42730.41916010.41916740.7450.7781000.169
2.276-2.3870.164820.15414970.15415790.9820.9831000.135
2.387-2.5160.16680.1414810.14115490.9850.9891000.127
2.516-2.6680.155630.14513560.14514190.9860.9881000.132
2.668-2.8510.174800.14112880.14313680.9820.9881000.135
2.851-3.0780.17710.13912120.14112830.9810.9871000.138
3.078-3.3690.156600.1311280.13111880.9850.991000.135
3.369-3.7630.141560.12410280.12510840.9920.9911000.133
3.763-4.3380.119510.1119250.1119760.9910.9931000.129
4.338-5.2960.111390.17930.1018320.9940.9951000.12
5.296-7.4170.185270.1396530.1416800.9840.991000.162
7.417-37.9040.185170.1594070.164240.9720.9781000.185

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