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- PDB-4d62: Structure of the carboxy-terminal domain of the turkey type 3 sia... -

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Basic information

Entry
Database: PDB / ID: 4d62
TitleStructure of the carboxy-terminal domain of the turkey type 3 siadenovirus fibre, avirulent form complexed with 3-sialyllactose.
ComponentsFIBER KNOB DOMAIN
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


symbiont entry into host cell / host cell nucleus / virion attachment to host cell
Similarity search - Function
Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) - #50 / Avian adenovirus fibre, N-terminal / Avian adenovirus fibre, N-terminal / Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) / Attachment protein shaft domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
N-acetyl-alpha-neuraminic acid / Fiber
Similarity search - Component
Biological speciesAVIRULENT TURKEY HEMORRHAGIC ENTERITIS VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.5 Å
AuthorsSingh, A.K. / van Raaij, M.J.
CitationJournal: PLoS ONE / Year: 2015
Title: Structure and Sialyllactose Binding of the Carboxy-Terminal Head Domain of the Fibre from a Siadenovirus, Turkey Adenovirus 3.
Authors: Singh, A.K. / Berbis, M.A. / Ballmann, M.Z. / Kilcoyne, M. / Menendez, M. / Nguyen, T.H. / Joshi, L. / Canada, F.J. / Jimenez-Barbero, J. / Benko, M. / Harrach, B. / van Raaij, M.J.
History
DepositionNov 8, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.page_first ..._citation.journal_abbrev / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation_author.name
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3May 8, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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: FIBER KNOB DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9212
Polymers20,6121
Non-polymers3091
Water32418
1
A: FIBER KNOB DOMAIN
hetero molecules

A: FIBER KNOB DOMAIN
hetero molecules

A: FIBER KNOB DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7646
Polymers61,8363
Non-polymers9283
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation5_555z,x,y1
Buried area8580 Å2
ΔGint-56.5 kcal/mol
Surface area16510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.310, 98.310, 98.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein FIBER KNOB DOMAIN / TURKEY ADENOVIRUS TYPE 3 FIBRE


Mass: 20611.973 Da / Num. of mol.: 1 / Fragment: HEAD DOMAIN, RESIDUES 15-165
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AVIRULENT TURKEY HEMORRHAGIC ENTERITIS VIRUS
Description: ARKO LABORATORIES, JEWELL IA, USA / Variant: AVIRULENT FORM / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2TLC1
#2: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID / Sialic acid


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 1.94 Å3/Da / Density % sol: 37 % / Description: NONE
Crystal growpH: 5.5
Details: 25 MM MORPHOLINO-ETHANESULFONIC ACID, 0.5-1.0M DIAMMONIUM PHOSPHATE, 0.1M SODIUM CITRATE PH 5.5-5.8, 0.2-0.3 M SODIUM CHLORIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 11, 2013
Details: TWO CYLINDRICAL VERTICAL FOCUSING PARABOLIC MIRRORS
RadiationMonochromator: SI (111), SI(311) DOUBLE CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. obs: 5355 / % possible obs: 100 % / Redundancy: 7.7 % / Biso Wilson estimate: 44.6 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.6
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.5→25 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.911 / SU B: 12.19 / SU ML: 0.256 / Cross valid method: THROUGHOUT / ESU R: 0.574 / ESU R Free: 0.297 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25413 261 4.6 %THIN SHELLS
Rwork0.19344 ---
obs0.19644 5355 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.906 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1092 0 21 18 1131
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191134
X-RAY DIFFRACTIONr_bond_other_d0.0010.021139
X-RAY DIFFRACTIONr_angle_refined_deg1.7111.991540
X-RAY DIFFRACTIONr_angle_other_deg0.77332612
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1345137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.15424.1346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.66415202
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.156157
X-RAY DIFFRACTIONr_chiral_restr0.0840.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211253
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02257
X-RAY DIFFRACTIONr_nbd_refined0.2090.2156
X-RAY DIFFRACTIONr_nbd_other0.1780.21122
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2532
X-RAY DIFFRACTIONr_nbtor_other0.0840.2675
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.227
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0330.22
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1480.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1930.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4185.035551
X-RAY DIFFRACTIONr_mcbond_other3.4215.024550
X-RAY DIFFRACTIONr_mcangle_it5.4577.523687
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.9215.566583
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.9838.179853
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.634 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.343 43 -
Rwork0.283 768 -
obs--100 %

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