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- PDB-5k7q: MicroED structure of thaumatin at 2.5 A resolution -

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Basic information

Entry
Database: PDB / ID: 5k7q
TitleMicroED structure of thaumatin at 2.5 A resolution
ComponentsThaumatin-1
KeywordsPLANT PROTEIN / Sweet protein
Function / homology
Function and homology information


cytoplasmic vesicle
Similarity search - Function
Thaumatin / Thaumatin / Thaumatin, conserved site / Thaumatin family signature. / Thaumatin family / Thaumatin family / Thaumatin family profile. / Thaumatin family / Osmotin/thaumatin-like superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesThaumatococcus daniellii (katemfe)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 2.5 Å
Authorsde la Cruz, M.J. / Hattne, J. / Shi, D. / Seidler, P. / Rodriguez, J. / Reyes, F.E. / Sawaya, M.R. / Cascio, D. / Eisenberg, D. / Gonen, T.
CitationJournal: Nat Methods / Year: 2017
Title: Atomic-resolution structures from fragmented protein crystals with the cryoEM method MicroED.
Authors: M Jason de la Cruz / Johan Hattne / Dan Shi / Paul Seidler / Jose Rodriguez / Francis E Reyes / Michael R Sawaya / Duilio Cascio / Simon C Weiss / Sun Kyung Kim / Cynthia S Hinck / Andrew P ...Authors: M Jason de la Cruz / Johan Hattne / Dan Shi / Paul Seidler / Jose Rodriguez / Francis E Reyes / Michael R Sawaya / Duilio Cascio / Simon C Weiss / Sun Kyung Kim / Cynthia S Hinck / Andrew P Hinck / Guillermo Calero / David Eisenberg / Tamir Gonen /
Abstract: Traditionally, crystallographic analysis of macromolecules has depended on large, well-ordered crystals, which often require significant effort to obtain. Even sizable crystals sometimes suffer from ...Traditionally, crystallographic analysis of macromolecules has depended on large, well-ordered crystals, which often require significant effort to obtain. Even sizable crystals sometimes suffer from pathologies that render them inappropriate for high-resolution structure determination. Here we show that fragmentation of large, imperfect crystals into microcrystals or nanocrystals can provide a simple path for high-resolution structure determination by the cryoEM method MicroED and potentially by serial femtosecond crystallography.
History
DepositionMay 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references
Revision 2.0Jul 18, 2018Group: Atomic model / Data collection / Category: atom_site / em_software / Item: _atom_site.occupancy / _em_software.name
Revision 2.1Aug 22, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set / Item: _pdbx_related_exp_data_set.data_reference
Revision 2.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Assembly

Deposited unit
A: Thaumatin-1


Theoretical massNumber of molelcules
Total (without water)22,2271
Polymers22,2271
Non-polymers00
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.118, 58.118, 150.307
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-312-

HOH

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Components

#1: Protein Thaumatin-1 / Thaumatin I


Mass: 22227.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thaumatococcus daniellii (katemfe) / References: UniProt: P02883
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: Thaumatin / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: NATURAL
Molecular weightValue: 0.022166 MDa / Experimental value: NO
Source (natural)Organism: Thaumatococcus daniellii (katemfe)
Buffer solutionpH: 7
Buffer componentConc.: 1.1 M / Name: ammonium tartate
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Data collection

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 4.1 sec. / Electron dose: 0.004 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Num. of diffraction images: 471 / Num. of grids imaged: 3 / Num. of real images: 471
Image scansSampling size: 0.0311999992 µm / Width: 2048 / Height: 2048
EM diffractionCamera length: 2000 mm
EM diffraction shellResolution: 2.5→2.86 Å / Fourier space coverage: 92.2 % / Multiplicity: 3.9 / Num. of structure factors: 2825 / Phase residual: 52.4 °
EM diffraction statsFourier space coverage: 81.5 % / High resolution: 2.11 Å / Num. of intensities measured: 51116 / Num. of structure factors: 12786 / Phase error: 28.74 ° / Phase residual: 41.7 ° / Phase error rejection criteria: 0 / Rmerge: 0.434 / Rsym: 0.434
ReflectionResolution: 2.11→27.73 Å / Num. all: 51116 / Num. obs: 12786 / % possible obs: 81.5 % / Redundancy: 4 % / Rmerge(I) obs: 0.434 / Rpim(I) all: 0.235 / Net I/σ(I): 2.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allNum. unique obsRpim(I) allNet I/σ(I) obs% possible all
2.11-2.172.50.86415636140.6361.248
8.93-27.7340.1838792210.0945.685.4

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Processing

SoftwareName: PHENIX / Version: (1.10_2155: ???) / Classification: refinement
EM software
IDNameVersionCategoryDetails
1EM-Menu4.0.9.75image acquisition
5iMosflm/MOSFLM7.2.1diffraction indexing
6MOLREP11.4.05model fitting
8PHENIX1.10_2155model refinement
9MOLREP11.4.05molecular replacementStarting model PDB ID 4ek0
11POINTLESS1.10.21symmetry determination
12AIMLESS0.5.25crystallography merging
EM 3D crystal entity∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 57.78 Å / B: 57.78 Å / C: 149.7 Å / Space group name: P41212 / Space group num: 92
CTF correctionType: NONE
3D reconstructionResolution: 2.5 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingProtocol: OTHER / Space: RECIPROCAL
Atomic model buildingPDB-ID: 4EK0

4ek0


Pdb chain-ID: A / Accession code: 4EK0 / Pdb chain residue range: 1-207 / Source name: PDB / Type: experimental model
RefinementResolution: 2.5→27.732 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2945 453 5.09 %
Rwork0.2513 --
obs0.2535 8898 93.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.0021595
ELECTRON CRYSTALLOGRAPHYf_angle_d0.4622168
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d12.505960
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.039230
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.004285
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.86150.38981350.34082690ELECTRON CRYSTALLOGRAPHY92
2.8615-3.6040.31271480.26362845ELECTRON CRYSTALLOGRAPHY96
3.604-27.73330.23841700.19592910ELECTRON CRYSTALLOGRAPHY93

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