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- PDB-4yn1: THE ATOMIC STRUCTURE OF ANOMALA CUPREA ENTOMOPOXVIRUS (ACEPV) FUS... -

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Basic information

Entry
Database: PDB / ID: 4yn1
TitleTHE ATOMIC STRUCTURE OF ANOMALA CUPREA ENTOMOPOXVIRUS (ACEPV) FUSOLIN SPINDLES
ComponentsFusolin
KeywordsVIRAL PROTEIN / INTRACELLULAR PROTEIN MICRO-CRYSTAL / CHITIN-B DOMAIN / STRUCTURAL PROTEIN / N-GLYCOSYLATION
Function / homologyCellulose/chitin-binding protein, N-terminal / Lytic polysaccharide mono-oxygenase, cellulose-degrading / Immunoglobulin E-set / Fusolin
Function and homology information
Biological speciesAnomala cuprea entomopoxvirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsChiu, E. / Bunker, R.D. / Metcalf, P.
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
DepositionMar 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / entity_src_nat ...citation / entity_src_nat / pdbx_struct_oper_list / pdbx_validate_close_contact / 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_struct_oper_list.symmetry_operation / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _software.classification
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_radiation_wavelength / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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)42,2746
Polymers41,4391
Non-polymers8355
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Fusolin
hetero molecules

A: Fusolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,54712
Polymers82,8782
Non-polymers1,67010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area8230 Å2
ΔGint13 kcal/mol
Surface area21610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.887, 71.887, 127.996
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-564-

HOH

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Components

#1: Protein Fusolin


Mass: 41438.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Anomala cuprea entomopoxvirus / References: UniProt: O70709
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2 Å3/Da / Density % sol: 38.35 %
Crystal growTemperature: 300 K / Method: in cell / pH: 7
Details: NATURALLY OCCURRING INTRACELLULAR FUSOLIN MICRO-CRYSTALS WERE PURIFIED FROM EPV-INFECTED LARVAE OF ANOMALA CUPREA MOTHS

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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: Dec 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→62.68 Å / Num. obs: 27160 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 17.5 % / Biso Wilson estimate: 18.27 Å2 / Rmerge(I) obs: 0.191 / Net I/σ(I): 12.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.699 / Mean I/σ(I) obs: 4 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
SHELXDEphasing
ARPmodel building
Cootmodel building
SHARPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BEM

2bem


Resolution: 1.9→62.68 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.921 / SU R Cruickshank DPI: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.122 / SU Rfree Blow DPI: 0.114 / SU Rfree Cruickshank DPI: 0.112
RfactorNum. reflection% reflectionSelection details
Rfree0.197 1324 4.99 %RANDOM
Rwork0.167 ---
obs0.168 25222 97.6 %-
Displacement parametersBiso mean: 20.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.1184 Å20 Å20 Å2
2--0.1184 Å20 Å2
3----0.2368 Å2
Refine analyzeLuzzati coordinate error obs: 0.153 Å
Refinement stepCycle: LAST / Resolution: 1.9→62.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2085 0 55 209 2349
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014241HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.047633HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d881SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes52HARMONIC2
X-RAY DIFFRACTIONt_gen_planes602HARMONIC5
X-RAY DIFFRACTIONt_it4241HARMONIC20
X-RAY DIFFRACTIONt_nbd8SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.47
X-RAY DIFFRACTIONt_other_torsion13.67
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion291SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4854SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.98 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.1795 131 4.61 %
Rwork0.1687 2713 -
all0.1692 2844 -
obs--97.58 %

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