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- PDB-4ow5: Structural basis for the enhancement of virulence by entomopoxvir... -

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Basic information

Entry
Database: PDB / ID: 4ow5
TitleStructural basis for the enhancement of virulence by entomopoxvirus fusolin and its in vivo crystallization into viral spindles
ComponentsFusolin
KeywordsVIRAL PROTEIN / Chitin-binding / LMPO / fibronectin type III fold
Function / homologyCellulose/chitin-binding protein, N-terminal / Lytic polysaccharide mono-oxygenase, cellulose-degrading / Immunoglobulin E-set / metal ion binding / Fusolin
Function and homology information
Biological speciesunidentified entomopoxvirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHijnen, M. / Boudes, M. / Aizel, K. / Coulibaly, F.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structural basis for the enhancement of virulence by viral spindles and their in vivo crystallization.
Authors: Chiu, E. / Hijnen, M. / Bunker, R.D. / Boudes, M. / Rajendran, C. / Aizel, K. / Olieric, V. / Schulze-Briese, C. / Mitsuhashi, W. / Young, V. / Ward, V.K. / Bergoin, M. / Metcalf, P. / Coulibaly, F.
History
DepositionJan 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references
Revision 1.2Apr 8, 2015Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / entity_src_nat ...citation / entity_src_nat / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_nat.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_nat.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: 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: Fusolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3298
Polymers43,8941
Non-polymers4347
Water3,549197
1
A: Fusolin
hetero molecules

A: Fusolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,65716
Polymers87,7882
Non-polymers86914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area7100 Å2
ΔGint-39 kcal/mol
Surface area28980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.270, 71.270, 129.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Fusolin


Mass: 43894.156 Da / Num. of mol.: 1 / Fragment: Chitin-binding domain / Mutation: G25D, H192N, I351N, I352H, Q353T, D354G / Source method: isolated from a natural source / Source: (natural) unidentified entomopoxvirus / References: UniProt: Q83389
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 26

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Sample preparation

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 34.57 %
Crystal growTemperature: 301 K / Method: in vivo crystallization / Details: crystals are obtained in vivo

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 17, 2011 / Details: Rh coated meridionally focussing mirror
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→28.6 Å / Num. obs: 26941 / % possible obs: 98.52 % / Redundancy: 13.9 % / Biso Wilson estimate: 20.31 Å2 / Rmerge(I) obs: 0.265 / Net I/σ(I): 10.6
Reflection shellResolution: 1.9→1.98 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.863 / Mean I/σ(I) obs: 1.9 / % possible all: 98.52

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.14data extraction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BEM

2bem


Resolution: 1.9→28.6 Å / Cor.coef. Fo:Fc: 0.9423 / Cor.coef. Fo:Fc free: 0.9268 / SU R Cruickshank DPI: 0.202 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.136 / SU Rfree Blow DPI: 0.124 / SU Rfree Cruickshank DPI: 0.122
RfactorNum. reflection% reflectionSelection details
Rfree0.2025 2721 10.2 %RANDOM
Rwork0.1677 ---
obs0.1712 26671 98.52 %-
Displacement parametersBiso max: 87.46 Å2 / Biso mean: 22.64 Å2 / Biso min: 4.94 Å2
Baniso -1Baniso -2Baniso -3
1--1.3703 Å20 Å20 Å2
2---1.3703 Å20 Å2
3---2.7405 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å
Refinement stepCycle: final / Resolution: 1.9→28.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2452 0 70 197 2719
Biso mean--38.89 36.67 -
Num. residues----307
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1301SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes74HARMONIC2
X-RAY DIFFRACTIONt_gen_planes737HARMONIC5
X-RAY DIFFRACTIONt_it4865HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion332SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance3HARMONIC1
X-RAY DIFFRACTIONt_utility_angle6HARMONIC1
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5681SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4865HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8706HARMONIC21
X-RAY DIFFRACTIONt_omega_torsion4.13
X-RAY DIFFRACTIONt_other_torsion2.83
LS refinement shellResolution: 1.9→1.98 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2697 296 10.98 %
Rwork0.2247 2401 -
all0.2296 2697 -
obs--98.52 %

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