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- PDB-7nji: HEX1 (in cellulo) loaded on HARE serial crystallography chip -

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Basic information

Entry
Database: PDB / ID: 7nji
TitleHEX1 (in cellulo) loaded on HARE serial crystallography chip
ComponentsWoronin body major protein
KeywordsSTRUCTURAL PROTEIN / serial crystallography / HEX1 / in-cellulo / silicon chip
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 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNorton-Baker, B. / Mehrabi, P. / Boger, J. / Schonherr, R. / von Stetten, D. / Schikora, H. / Martin, R.W. / Miller, R.J.D. / Redecke, L. / Schulz, E.C.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: A simple vapor-diffusion method enables protein crystallization inside the HARE serial crystallography chip.
Authors: Norton-Baker, B. / Mehrabi, P. / Boger, J. / Schonherr, R. / von Stetten, D. / Schikora, H. / Kwok, A.O. / Martin, R.W. / Miller, R.J.D. / Redecke, L. / Schulz, E.C.
History
DepositionFeb 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
Water50428
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 area2400 Å2
ΔGint-8 kcal/mol
Surface area15240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.900, 58.900, 193.000
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-228-

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 (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (fungus)
Strain: ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987
Gene: hex-1, NCU08332 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P87252
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.52 Å3/Da / Density % sol: 51.25 %
Crystal growTemperature: 300 K / Method: in cell
Details: Grown inside Spodoptera frugiperda Sf9 insect cells

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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: 0.9762 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.3→86.94 Å / Num. obs: 9522 / % possible obs: 100 % / Redundancy: 93 % / Biso Wilson estimate: 40.33 Å2 / CC1/2: 0.9087 / Net I/σ(I): 3.2
Reflection shellResolution: 2.3→2.382 Å / Num. unique obs: 917 / CC1/2: 0.3817
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KHI

1khi


Resolution: 2.3→51.01 Å / SU ML: 0.3218 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.012
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2601 448 4.71 %
Rwork0.2193 9073 -
obs0.2212 9521 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.52 Å2
Refinement stepCycle: LAST / Resolution: 2.3→51.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1128 0 0 28 1156
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00961147
X-RAY DIFFRACTIONf_angle_d1.15751553
X-RAY DIFFRACTIONf_chiral_restr0.0637182
X-RAY DIFFRACTIONf_plane_restr0.0062201
X-RAY DIFFRACTIONf_dihedral_angle_d15.1206157
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.630.34361440.29172917X-RAY DIFFRACTION100
2.63-3.320.25551280.26122993X-RAY DIFFRACTION100
3.32-51.010.24391760.18563163X-RAY DIFFRACTION99.94

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