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- PDB-8qlw: Purpureocillium lilancinum Woronin Body Major protein crystallize... -

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Basic information

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


positive regulation of 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-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 speciesPurpureocillium lilacinum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsBoger, J. / Redecke, L.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research05K18FLA Germany
CitationJournal: To Be Published
Title: Purpureocillium lilancinum Woronin Body Major protein crystallized in cellulo
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

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Assembly

Deposited unit
A: Woronin body major protein


Theoretical massNumber of molelcules
Total (without water)23,3881
Polymers23,3881
Non-polymers00
Water1,38777
1
A: Woronin body major protein

A: Woronin body major protein


Theoretical massNumber of molelcules
Total (without water)46,7772
Polymers46,7772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Buried area3440 Å2
ΔGint-12 kcal/mol
Surface area16710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.100, 57.100, 200.340
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

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Components

#1: Protein Woronin body major protein


Mass: 23388.451 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Purpureocillium lilacinum (fungus) / Gene: PCL_00196 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A2U3E6B3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.02 Å3/Da / Density % sol: 38.97 %
Crystal growTemperature: 300 K / Method: in cell
Details: spontaneous crystallization in living High Five cells after recombinant expression using baculoviruses

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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: 1.97→66.78 Å / Num. obs: 14631 / % possible obs: 100 % / Redundancy: 1211 % / Biso Wilson estimate: 31.53 Å2 / CC1/2: 0.9989 / Net I/σ(I): 18.27
Reflection shellResolution: 1.97→1.99 Å / Num. unique obs: 684 / CC1/2: 0.1924

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→49.45 Å / SU ML: 0.2594 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.786
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2361 2564 9.93 %
Rwork0.2002 23263 -
obs0.2038 14531 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.58 Å2
Refinement stepCycle: LAST / Resolution: 1.97→49.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1343 0 0 77 1420
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00321374
X-RAY DIFFRACTIONf_angle_d0.65431864
X-RAY DIFFRACTIONf_chiral_restr0.0493205
X-RAY DIFFRACTIONf_plane_restr0.0072245
X-RAY DIFFRACTIONf_dihedral_angle_d5.0981190
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.010.39911400.39111277X-RAY DIFFRACTION99.93
2.01-2.050.35811410.30681295X-RAY DIFFRACTION100
2.05-2.090.3141500.29281286X-RAY DIFFRACTION100
2.09-2.140.2851400.25511288X-RAY DIFFRACTION100
2.14-2.20.25741470.24241324X-RAY DIFFRACTION99.93
2.2-2.250.30371420.22291273X-RAY DIFFRACTION100
2.26-2.320.28251370.21121279X-RAY DIFFRACTION100
2.32-2.40.29661440.21191309X-RAY DIFFRACTION100
2.4-2.480.30581460.20631306X-RAY DIFFRACTION100
2.48-2.580.22981390.22451276X-RAY DIFFRACTION100
2.58-2.70.26011410.21361293X-RAY DIFFRACTION100
2.7-2.840.26291440.22031304X-RAY DIFFRACTION100
2.84-3.020.24951420.20241289X-RAY DIFFRACTION99.93
3.02-3.250.24651440.19481269X-RAY DIFFRACTION100
3.25-3.580.2221410.17471319X-RAY DIFFRACTION100
3.58-4.090.20211460.16131289X-RAY DIFFRACTION100
4.1-5.160.16481420.14361288X-RAY DIFFRACTION100
5.17-49.450.21471380.21411299X-RAY DIFFRACTION99.93
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)
11.854881759110.8626882925591.174596993112.224615098181.131222529963.07636275898-0.0345263977153-0.1297160973320.1345265024750.0984383149585-0.0380190861238-0.0679202061318-0.2379689923020.09611900118620.06291260688410.222594549622-0.02613924483460.01554258743710.2512159700640.01037086964940.23351671297534.353917376532.73182668742.6515456427
24.55710825566-5.38535829803-1.1732766859.48689648273-0.1217829781841.473013838370.04727947230960.249823313544-0.253142312154-0.2193157737850.003005378292770.3192127907970.179177376619-0.0710060754547-0.08082337780620.224744757674-0.0153792360935-0.0205102407710.2872345552110.0008530022360650.2228143401077.5760616178528.924499508435.1361348549
35.00300332854-0.6007906956911.011327886748.373848833530.2130083285374.905774928010.0241696747281-0.381947623325-0.2205804143340.5116837168750.01518542598240.06636191806230.0805826220169-0.414089111431-0.08014418501590.1479977779340.04556101047490.008223133329820.2805611530810.005897655089090.235836026459.8752611647724.926566137338.9962626012
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 0 through 123 )0 - 1231 - 105
22chain 'A' and (resid 124 through 156 )124 - 156106 - 138
33chain 'A' and (resid 157 through 193 )157 - 193139 - 175

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