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- PDB-8qlu: Aspergillus fumigatus Woronin Body Major protein crystallized in ... -

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Basic information

Entry
Database: PDB / ID: 8qlu
TitleAspergillus fumigatus Woronin Body Major protein crystallized in cellulo
ComponentsWoronin body major protein hexA
KeywordsSTRUCTURAL PROTEIN / self-assembly / natively crystallizing / HEX-1 / Woronin Body Major Protein
Function / homology
Function and homology information


porous cell septum / Woronin body / positive regulation of translational elongation / translational elongation / translation elongation factor activity / response to wounding / ribosome binding / RNA binding
Similarity search - Function
Hex1, S1 domain / 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 hexA
Similarity search - Component
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsBoger, J. / Redecke, L.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research05K18FLA Germany
CitationJournal: To Be Published
Title: HEX-1 protein structures in comparison
Authors: Boger, J. / Redecke, L.
History
DepositionSep 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Woronin body major protein hexA


Theoretical massNumber of molelcules
Total (without water)24,8101
Polymers24,8101
Non-polymers00
Water1,24369
1
A: Woronin body major protein hexA

A: Woronin body major protein hexA


Theoretical massNumber of molelcules
Total (without water)49,6202
Polymers49,6202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Buried area1830 Å2
ΔGint-10 kcal/mol
Surface area14430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.360, 58.360, 190.050
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-248-

HOH

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Components

#1: Protein Woronin body major protein hexA


Mass: 24810.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Gene: hexA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q4WUL0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 3.02 Å3/Da / Density % sol: 59.31 %
Crystal growTemperature: 300 K / Method: in cell
Details: spontaneous crystallization in cellulo in T.ni High Five cells after recombinant expression using the DH10EmBacY baculovirus expression system

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.02→63.35 Å / Num. obs: 13432 / % possible obs: 99.64 % / Redundancy: 245.8 % / Biso Wilson estimate: 29.66 Å2 / CC1/2: 0.9962 / Net I/σ(I): 12.92
Reflection shellResolution: 2.02→2.04 Å / Num. unique obs: 633 / CC1/2: 0.219

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→50.54 Å / SU ML: 0.2276 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.5219
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2292 2350 9.97 %
Rwork0.2169 21213 -
obs0.2181 13270 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.6 Å2
Refinement stepCycle: LAST / Resolution: 2.02→50.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1031 0 0 69 1100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00161064
X-RAY DIFFRACTIONf_angle_d0.44931449
X-RAY DIFFRACTIONf_chiral_restr0.047177
X-RAY DIFFRACTIONf_plane_restr0.0041185
X-RAY DIFFRACTIONf_dihedral_angle_d4.2674149
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.060.3291210.36751157X-RAY DIFFRACTION91.61
2.06-2.110.33171420.34171212X-RAY DIFFRACTION96.58
2.11-2.160.38471410.31921242X-RAY DIFFRACTION98.79
2.16-2.210.40611330.29661248X-RAY DIFFRACTION99.64
2.21-2.270.24981380.27491255X-RAY DIFFRACTION99.93
2.27-2.340.24861460.26021277X-RAY DIFFRACTION100
2.34-2.410.221440.23241237X-RAY DIFFRACTION100
2.41-2.50.22521380.2181247X-RAY DIFFRACTION100
2.5-2.60.22361400.2121258X-RAY DIFFRACTION100
2.6-2.710.221350.21631259X-RAY DIFFRACTION99.93
2.72-2.860.24181360.20831258X-RAY DIFFRACTION100
2.86-3.040.24831400.20651265X-RAY DIFFRACTION100
3.04-3.270.22191360.20931275X-RAY DIFFRACTION100
3.27-3.60.21181390.21248X-RAY DIFFRACTION100
3.6-4.120.17381430.17451252X-RAY DIFFRACTION100
4.12-5.190.16061360.16421257X-RAY DIFFRACTION99.93
5.19-50.540.25391420.22711266X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.12336854960.8155509932951.644464758453.952025263160.946941849854.44693967743-0.03953658544050.004037764028320.01665736521090.01924505090.0257933549527-0.0218270961266-0.107334790320.04119862996280.04495133242890.138686383825-0.01971407831260.008899153670980.1650134150720.01142069217230.16821268425234.498462144529.078296310538.0171068223
28.51499830676-2.542025638923.611937847884.182969168310.838998464685.859090676250.17818926790.266029830598-0.7357873452010.0396786460823-0.1207871949930.4740218037620.215279527118-0.137490030865-0.002516942639170.1878223814250.02716720365430.0009212865024740.306796270739-0.005406456361980.3162432730769.0739251428128.010802688734.5328071073
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 31 through 103 )31 - 1031 - 73
22chain 'A' and (resid 104 through 172 )104 - 17274 - 137

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