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- PDB-8c5k: HEX-1 (in cellulo, in situ) crystallized and diffracted in High F... -

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Basic information

Entry
Database: PDB / ID: 8c5k
TitleHEX-1 (in cellulo, in situ) crystallized and diffracted in High Five cells. Growth and SX data collection at 296 K on CrystalDirect plates
ComponentsWoronin body major protein
KeywordsSTRUCTURAL PROTEIN / Woronin body / self-assembly / HEX-1 / in vivo
Function / homology
Function and homology information


Woronin body / positive regulation of translational termination / positive regulation of translational elongation / cell septum / translational elongation / translation elongation factor activity / ribosome binding / RNA binding
Similarity search - Function
Hex1, S1 domain / : / Translation initiation factor 5A-like, N-terminal / Translation elongation factor, IF5A C-terminal / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / Translation elongation factor IF5A-like / Translation protein SH3-like domain superfamily / Ribosomal protein L2, domain 2 / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Woronin body major protein
Similarity search - Component
Biological speciesNeurospora crassa OR74A (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsLahey-Rudolph, J.M. / Schoenherr, R. / Boger, J. / Harms, M. / Kaiser, J. / Nachtschatt, S. / Wobbe, M. / Duden, R. / Koenig, P. / Bourenkov, G. ...Lahey-Rudolph, J.M. / Schoenherr, R. / Boger, J. / Harms, M. / Kaiser, J. / Nachtschatt, S. / Wobbe, M. / Duden, R. / Koenig, P. / Bourenkov, G. / Schneider, T. / Redecke, L.
Funding support Germany, 2items
OrganizationGrant numberCountry
Joachim Herz StiftungPhD scholarship Germany
German Research Foundation (DFG)EXC306 Germany
CitationJournal: Nat Commun / Year: 2024
Title: A streamlined approach to structure elucidation using in cellulo crystallized recombinant proteins, InCellCryst.
Authors: Schonherr, R. / Boger, J. / Lahey-Rudolph, J.M. / Harms, M. / Kaiser, J. / Nachtschatt, S. / Wobbe, M. / Duden, R. / Konig, P. / Bourenkov, G. / Schneider, T.R. / Redecke, L.
History
DepositionJan 9, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Woronin body major protein


Theoretical massNumber of molelcules
Total (without water)19,1511
Polymers19,1511
Non-polymers00
Water41423
1
A: Woronin body major protein

A: Woronin body major protein


Theoretical massNumber of molelcules
Total (without water)38,3012
Polymers38,3012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Buried area1920 Å2
ΔGint-6 kcal/mol
Surface area14870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.650, 58.650, 191.450
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-220-

HOH

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Components

#1: Protein Woronin body major protein


Mass: 19150.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa OR74A (fungus) / Strain: ATCC 24698 / Gene: hex-1, NCU08332 / Plasmid: pFB1 / Details (production host): cyto / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P87252
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O

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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: 2.49 Å3/Da / Density % sol: 50.59 % / Description: hexagonal, spindle-like shape
Crystal growTemperature: 300 K / Method: in cell
Details: Infected with rBV HEX-1 and grown in High-Five cells in suspension culture, MOI 1

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.971 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.971 Å / Relative weight: 1
ReflectionResolution: 2.16→49.09 Å / Num. obs: 11210 / % possible obs: 99.96 % / Redundancy: 246 % / Biso Wilson estimate: 24.1 Å2 / CC1/2: 0.998 / CC star: 0.999 / R split: 0.0586 / Net I/σ(I): 10.41
Reflection shellResolution: 2.16→2.237 Å / Redundancy: 68 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1066 / CC1/2: 0.595 / CC star: 0.864 / R split: 0.871 / % possible all: 99.72
Serial crystallography sample deliveryDescription: CrystalDirect plate (96 well) / Method: fixed target
Serial crystallography sample delivery fixed targetDescription: in cellulo in situ growth
Details: 90 degree mounting of Crystal Direct plate on goniometer, well polymer foil coating with D-lys
Sample dehydration prevention: crystallization foil seal / Sample holding: CrystalDirect / Sample solvent: ESF921 insect cell medium with 25% FBS / Support base: goniometer
Serial crystallography data reductionCrystal hits: 91354 / Frames indexed: 55640 / Frames total: 595419 / Lattices indexed: 57052

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158-000refinement
CrystFEL0.10.0data scaling
Coot0.9.7model building
PHASER1.19.2-4158-000phasing
CrystFEL0.9.1data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1khi

1khi


Resolution: 2.16→49.09 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2328 1120 9.99 %
Rwork0.1816 --
obs0.1866 11208 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.16→49.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1093 0 0 23 1116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161119
X-RAY DIFFRACTIONf_angle_d1.2631518
X-RAY DIFFRACTIONf_dihedral_angle_d6.318153
X-RAY DIFFRACTIONf_chiral_restr0.072180
X-RAY DIFFRACTIONf_plane_restr0.011196
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection Rwork
2.16-2.260.34371340.31011216
2.26-2.380.27861339.990.26571200
2.38-2.530.32221370.23971230
2.53-2.720.27051370.22331236
2.72-2.990.27361390.20461247
3-3.430.2671400.19611261
3.43-4.320.20671440.15271291
4.32-49.090.19181560.1531407

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