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- PDB-8a9f: Thaumatin, 9-11 fs FEL pulses as determined by XTCAV -

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Basic information

Entry
Database: PDB / ID: 8a9f
TitleThaumatin, 9-11 fs FEL pulses as determined by XTCAV
ComponentsThaumatin-1
KeywordsANTIFUNGAL PROTEIN / free electron laser / radiation damage / disulfide bond
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 / FREE ELECTRON LASER / FOURIER SYNTHESIS / Resolution: 1.88 Å
AuthorsBarends, T. / Nass, K. / Gorel, A. / Schlichting, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: To Be Published
Title: Microcrystallization paper
Authors: Gorel, A. / Nass, K. / Barends, T. / Schlichting, I.
History
DepositionJun 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 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
AAA: Thaumatin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3772
Polymers22,2271
Non-polymers1501
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.250, 58.250, 150.600
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


Mass: 22227.059 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.: 132 / 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: 2.87 Å3/Da / Density % sol: 57.2 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 7
Details: 0.8 M NA, K TARTRATE, 0.1 M NA HEPES PH 7.0, BATCH MODE, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.338 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Apr 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.338 Å / Relative weight: 1
ReflectionResolution: 1.88→23.12 Å / Num. obs: 21989 / % possible obs: 100 % / Redundancy: 1 % / CC1/2: 0.955 / CC star: 0.989 / R split: 0.219 / Net I/σ(I): 3.5
Reflection shellResolution: 1.88→1.93 Å / % possible obs: 100 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1053 / CC1/2: 0.426 / CC star: 0.773 / R split: 0.97
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
CrystFELdata reduction
CrystFELdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5FGT

5fgt


Resolution: 1.88→22.67 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.765 / SU ML: 0.1 / Cross valid method: FREE R-VALUE / ESU R: 0.115 / ESU R Free: 0.111
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2038 1022 4.663 %
Rwork0.1727 20896 -
all0.174 --
obs-21918 90.939 %
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: 24.826 Å2
Baniso -1Baniso -2Baniso -3
1-0.251 Å2-0 Å2-0 Å2
2--0.251 Å2-0 Å2
3----0.502 Å2
Refinement stepCycle: LAST / Resolution: 1.88→22.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1550 0 10 132 1692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131614
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171415
X-RAY DIFFRACTIONr_angle_refined_deg1.6591.6692197
X-RAY DIFFRACTIONr_angle_other_deg1.421.5853294
X-RAY DIFFRACTIONr_dihedral_angle_1_deg20.125.394216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.91121.05376
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82515240
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg7.723153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5871512
X-RAY DIFFRACTIONr_chiral_restr0.0680.2215
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022059
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02361
X-RAY DIFFRACTIONr_nbd_refined0.1960.2283
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.21314
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2797
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.2812
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.2123
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2150.211
X-RAY DIFFRACTIONr_nbd_other0.2080.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1660.210
X-RAY DIFFRACTIONr_mcbond_it2.0092.357831
X-RAY DIFFRACTIONr_mcbond_other1.9322.353830
X-RAY DIFFRACTIONr_mcangle_it2.9593.5281038
X-RAY DIFFRACTIONr_mcangle_other2.9583.5341039
X-RAY DIFFRACTIONr_scbond_it3.3552.751783
X-RAY DIFFRACTIONr_scbond_other3.362.754780
X-RAY DIFFRACTIONr_scangle_it5.2093.9461157
X-RAY DIFFRACTIONr_scangle_other5.2113.9471156
X-RAY DIFFRACTIONr_lrange_it6.99428.1551792
X-RAY DIFFRACTIONr_lrange_other6.80627.871767
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.926-1.9810.371740.2861549X-RAY DIFFRACTION100
1.981-2.0420.296780.2721501X-RAY DIFFRACTION100
2.042-2.1080.288660.2481469X-RAY DIFFRACTION100
2.108-2.1810.286740.2311423X-RAY DIFFRACTION100
2.181-2.2630.2650.2071383X-RAY DIFFRACTION100
2.263-2.3540.226590.2011331X-RAY DIFFRACTION100
2.354-2.4580.215660.1911264X-RAY DIFFRACTION99.9249
2.458-2.5770.226680.2011207X-RAY DIFFRACTION100
2.577-2.7140.215560.191170X-RAY DIFFRACTION100
2.714-2.8760.175490.1641115X-RAY DIFFRACTION100
2.876-3.0710.184520.1561066X-RAY DIFFRACTION100
3.071-3.3120.173480.156972X-RAY DIFFRACTION100
3.312-3.6210.219450.141925X-RAY DIFFRACTION100
3.621-4.0360.145380.132828X-RAY DIFFRACTION100
4.036-4.6370.129390.108758X-RAY DIFFRACTION100
4.637-5.6220.154330.121642X-RAY DIFFRACTION100
5.622-7.7240.163250.132538X-RAY DIFFRACTION100

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