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

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Basic information

Entry
Database: PDB / ID: 3zpf
TitleStructure of the carboxy-terminal domain of the turkey type 3 siadenovirus fibre
ComponentsFIBER
KeywordsVIRAL PROTEIN / TURKEY HEMORRHAGIC ENTERITIS VIRUS / BETA-SANDWICH
Function / homology
Function and homology information


symbiont entry into host cell / virion attachment to host cell / host cell nucleus
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
PHOSPHATE ION / Fiber
Similarity search - Component
Biological speciesAVIRULENT TURKEY HEMORRHAGIC ENTERITIS VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 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
DepositionFeb 27, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Jan 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 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: FIBER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4472
Polymers21,3521
Non-polymers951
Water84747
1
A: FIBER
hetero molecules

A: FIBER
hetero molecules

A: FIBER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3426
Polymers64,0573
Non-polymers2853
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation5_555z,x,y1
Buried area7060 Å2
ΔGint-62.2 kcal/mol
Surface area17490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.750, 98.750, 98.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-2045-

HOH

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Components

#1: Protein FIBER / TURKEY ADENOVIRUS TYPE 3 FIBRE


Mass: 21352.236 Da / Num. of mol.: 1 / Fragment: HEAD DOMAIN, RESIDUES 301-454
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AVIRULENT TURKEY HEMORRHAGIC ENTERITIS VIRUS
Strain: AVIRULENT HEMORRHAGIC ENTERITIS VACCINE, LIVE VIRUS / Description: ARKO LABORATORIES, JEWELL IA, USA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2TLC1
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 5.8
Details: 25 MM MORPHOLINO-ETHANESULFONIC ACID, 0.5-1.0 M DIAMMONIUM PHOSPHATE, 0.1 M 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: ID14-4 / Wavelength: 0.9791
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 26, 2012 / Details: TOROIDAL FOCUSING MIRROR
RadiationMonochromator: CHANNEL CUT ESRF MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 8297 / % possible obs: 100 % / Redundancy: 43.2 % / Biso Wilson estimate: 46 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 29
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 43.1 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 6.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.2→28.51 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / SU B: 6.134 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.271 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25154 385 4.6 %RANDOM
Rwork0.20701 ---
obs0.20918 7909 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.073 Å2
Refinement stepCycle: LAST / Resolution: 2.2→28.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1092 0 5 47 1144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221117
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.9731515
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.255137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.80324.1346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.24915202
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.818157
X-RAY DIFFRACTIONr_chiral_restr0.0910.2178
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021819
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.230.2395
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.2743
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.259
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0311.5689
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.92521133
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6263428
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2154.5382
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: 2.2→2.319 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.295 56 -
Rwork0.254 1145 -
obs--100 %

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