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- PDB-9ftv: Serial microseconds crystallography at ID29 using MPI extruder: T... -

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Basic information

Entry
Database: PDB / ID: 9ftv
TitleSerial microseconds crystallography at ID29 using MPI extruder: Thaumatin
ComponentsThaumatin I
KeywordsPLANT PROTEIN / Serial Crystallography / serial microsecond crystallography / room temperature / ID29 / ESRF-EBS
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: 1.75 Å
AuthorsOrlans, J. / Rose, S.L. / Basu, S. / de Sanctis, D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Commun Chem / Year: 2025
Title: Advancing macromolecular structure determination with microsecond X-ray pulses at a 4th generation synchrotron.
Authors: Orlans, J. / Rose, S.L. / Ferguson, G. / Oscarsson, M. / Homs Puron, A. / Beteva, A. / Debionne, S. / Theveneau, P. / Coquelle, N. / Kieffer, J. / Busca, P. / Sinoir, J. / Armijo, V. / Lopez ...Authors: Orlans, J. / Rose, S.L. / Ferguson, G. / Oscarsson, M. / Homs Puron, A. / Beteva, A. / Debionne, S. / Theveneau, P. / Coquelle, N. / Kieffer, J. / Busca, P. / Sinoir, J. / Armijo, V. / Lopez Marrero, M. / Felisaz, F. / Papp, G. / Gonzalez, H. / Caserotto, H. / Dobias, F. / Gigmes, J. / Lebon, G. / Basu, S. / de Sanctis, D.
History
DepositionJun 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2025Provider: 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)22,3782
Polymers22,2281
Non-polymers1501
Water3,225179
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.490, 58.490, 151.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Thaumatin I / Thaumatin-1


Mass: 22228.043 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.: 179 / 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: 56 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 1.8 M Sodium Potassium Tartrate

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.072 Å
DetectorType: PSI JUNGFRAU 4M / Detector: PIXEL / Date: Apr 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 1.75→54.56 Å / Num. obs: 27502 / % possible obs: 100 % / Redundancy: 2001 % / Biso Wilson estimate: 21.99 Å2 / CC star: 0.9993 / R split: 0.0423 / Net I/σ(I): 22.25
Reflection shellResolution: 1.75→1.78 Å / Num. unique obs: 1339 / CC star: 0.9508 / R split: 0.3892
Serial crystallography sample deliveryDescription: MPI extruder / Method: injection

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→46.28 Å / SU ML: 0.1642 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.2339
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1699 1998 7.29 %
Rwork0.14 25411 -
obs0.1422 27409 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.07 Å2
Refinement stepCycle: LAST / Resolution: 1.75→46.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1521 0 10 179 1710
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00621599
X-RAY DIFFRACTIONf_angle_d0.85822185
X-RAY DIFFRACTIONf_chiral_restr0.0589241
X-RAY DIFFRACTIONf_plane_restr0.007290
X-RAY DIFFRACTIONf_dihedral_angle_d13.1389567
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.27191400.23281770X-RAY DIFFRACTION100
1.79-1.840.24191400.18531786X-RAY DIFFRACTION100
1.84-1.90.19841390.16111773X-RAY DIFFRACTION100
1.9-1.960.19581400.14831785X-RAY DIFFRACTION100
1.96-2.030.19381400.15531780X-RAY DIFFRACTION100
2.03-2.110.19731400.14461777X-RAY DIFFRACTION100
2.11-2.20.19351410.14261780X-RAY DIFFRACTION99.95
2.2-2.320.18491420.14181807X-RAY DIFFRACTION100
2.32-2.470.16751430.14141809X-RAY DIFFRACTION99.95
2.47-2.660.1931430.15681813X-RAY DIFFRACTION99.85
2.66-2.920.18481410.16081814X-RAY DIFFRACTION99.95
2.92-3.350.16811460.14821834X-RAY DIFFRACTION100
3.35-4.220.141460.11461882X-RAY DIFFRACTION99.85
4.22-46.280.1331570.11682001X-RAY DIFFRACTION99.95

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