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- PDB-3vsn: The crystal structure of novel chondroition lyase ODV-E66, baculo... -

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Basic information

Entry
Database: PDB / ID: 3vsn
TitleThe crystal structure of novel chondroition lyase ODV-E66, baculovirus envelope protein
ComponentsOcclusion-derived virus envelope protein E66
KeywordsLYASE ACTIVATOR / alpha/alpha troid / beta-sandwich
Function / homology
Function and homology information


Lyases; Carbon-oxygen lyases; Acting on polysaccharides / host cell cytoplasm / lyase activity / viral envelope / host cell nucleus / virion membrane / membrane
Similarity search - Function
Immunoglobulin-like - #4340 / Baculovirus E66 occlusion-derived virus envelope protein, domain 2 / Baculovirus occlusion-derived virus envelope, E66 / Baculovirus occlusion-derived virus envelope, E66, core domain / Baculovirus E66 occlusion-derived virus envelope protein / Polysaccharide lyase 8, N-terminal alpha-helical / Polysaccharide lyase family 8, N terminal alpha-helical domain / Chondroitin AC/alginate lyase / Chondroitin AC/alginate lyase / Beta-galactosidase; Chain A, domain 5 ...Immunoglobulin-like - #4340 / Baculovirus E66 occlusion-derived virus envelope protein, domain 2 / Baculovirus occlusion-derived virus envelope, E66 / Baculovirus occlusion-derived virus envelope, E66, core domain / Baculovirus E66 occlusion-derived virus envelope protein / Polysaccharide lyase 8, N-terminal alpha-helical / Polysaccharide lyase family 8, N terminal alpha-helical domain / Chondroitin AC/alginate lyase / Chondroitin AC/alginate lyase / Beta-galactosidase; Chain A, domain 5 / Glycosyltransferase / Alpha/alpha barrel / Distorted Sandwich / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
IODIDE ION / Non-sulfated chondroitin lyase E66
Similarity search - Component
Biological speciesAutographa californica nucleopolyhedrovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsKawaguchi, Y. / Sugiura, N. / Kimata, K. / Kimura, M. / Kakuta, Y.
Citation
Journal: To be Published
Title: The crystal structure of novel chondroition lyase ODV-E66, baculovirus envelope protein
Authors: Kawaguchi, Y. / Sugiura, N. / Kimata, K. / Kimura, M. / Kakuta, Y.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Crystallization and X-ray diffraction analysis of chondroitin lyase from baculovirus: envelope protein ODV-E66.
Authors: Kawaguchi, Y. / Sugiura, N. / Onishi, M. / Kimata, K. / Kimura, M. / Kakuta, Y.
History
DepositionApr 27, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Occlusion-derived virus envelope protein E66
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,62384
Polymers74,3681
Non-polymers10,25583
Water10,881604
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.172, 118.172, 100.099
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein Occlusion-derived virus envelope protein E66 / ODV-E66


Mass: 74368.164 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 67-704
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Autographa californica nucleopolyhedrovirus
Gene: P79 / Production host: Escherichia coli (E. coli) / References: UniProt: Q00704
#2: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 75 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 604 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE EXPERIMENTAL INFO OF UNIPROT (Q00704, OE66_NPVAC) SHOWS CONFLICT AT THIS POSITION: I -> M

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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: 2.71 Å3/Da / Density % sol: 54.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50mM Tri-HCl pH8.0, 100mM NaCl, 0.02M citric acid, 0.08M Bis-Tris propane pH8.8, 18% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1.3 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 86407 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Rmerge(I) obs: 0.133

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2→8.74 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.876 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19421 2593 4.9 %RANDOM
Rwork0.1664 ---
obs0.16775 49870 97.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.671 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→8.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5031 0 123 604 5758
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.025234
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0461.9347140
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5735643
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.55324.38258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.7215805
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5181527
X-RAY DIFFRACTIONr_chiral_restr0.0750.2795
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214058
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.049 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.209 183 -
Rwork0.177 3381 -
obs--97.43 %

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