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- PDB-4ue0: Structure of the bovine atadenovirus type 4 fibre head protein -

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Basic information

Entry
Database: PDB / ID: 4ue0
TitleStructure of the bovine atadenovirus type 4 fibre head protein
ComponentsFIBER
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


adhesion receptor-mediated virion attachment to host cell / viral capsid / cell adhesion / symbiont entry into host cell / host cell nucleus / nucleus
Similarity search - Function
Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein / Attachment protein shaft domain superfamily
Similarity search - Domain/homology
CARBONATE ION / THIOCYANATE ION / Fiber
Similarity search - Component
Biological speciesBOVINE ADENOVIRUS 4
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.17 Å
AuthorsNguyen, T.H. / van Raaij, M.J.
CitationJournal: Virol. J. / Year: 2015
Title: Crystal structure of the fibre head domain of bovine adenovirus 4, a ruminant atadenovirus.
Authors: Nguyen, T.H. / Vidovszky, M.Z. / Ballmann, M.Z. / Sanz-Gaitero, M. / Singh, A.K. / Harrach, B. / Benko, M. / van Raaij, M.J.
History
DepositionDec 14, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_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

Downloads & links

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Assembly

Deposited unit
A: FIBER
B: FIBER
C: FIBER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8035
Polymers40,6843
Non-polymers1182
Water7,945441
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-19.6 kcal/mol
Surface area15360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.330, 48.190, 52.070
Angle α, β, γ (deg.)117.11, 95.56, 110.17
Int Tables number1
Space group name H-MP1

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Components

#1: Protein FIBER /


Mass: 13561.470 Da / Num. of mol.: 3 / Fragment: HEAD DOMAIN, RESIDUES 414-535
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOVINE ADENOVIRUS 4
Description: PROTOTYPE STRAIN OF BADV-4 (CALLED THT/62) WAS ISOLATED BY ADORJAN BARTHA IN 1962. THE GENOME IN THE GENBANK IS UNDER ACCESSION NUMBER NC_002685.2. IT IS A SO CALLED REFSEQ ENTRY, ...Description: PROTOTYPE STRAIN OF BADV-4 (CALLED THT/62) WAS ISOLATED BY ADORJAN BARTHA IN 1962. THE GENOME IN THE GENBANK IS UNDER ACCESSION NUMBER NC_002685.2. IT IS A SO CALLED REFSEQ ENTRY, MEANING THAT BADV-4 IS THE REFERENCE STRAIN FOR THE BOVINE ATADENOVIRUS D SPECIES. REFERENCE BARTHA, A., ALDASY, P. (1966) FURTHER TWO SEROTYPES OF BOVINE ADENOVIRUS (SEROTYPE 4 AND 5). ACTA VET. HUNG. ACAD. SCI. 16(1)107-108.
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): JM109 / References: UniProt: Q997H2
#2: Chemical ChemComp-CO3 / CARBONATE ION / Carbonate


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#3: Chemical ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 441 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44 % / Description: NONE
Crystal growDetails: 20% (W/V) PEG3350, 200 MM KSCN, 50 MM NACL, 10 MM TRIS-HCL PH 7.5, 5% (V/V) GLYCEROL
PH range: 7.5; 7.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONESRF ID2910.9763
SYNCHROTRONALBA XALOC21.0023
Detector
TypeIDDetectorDateDetails
DECTRIS PILATUS 6M1PIXELFeb 21, 2014CYLINDRICAL GRAZING
DECTRIS PILATUS 6M2PIXELJan 31, 2014CYLINDRICAL GRAZING
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1LIQUID NITROGEN COOLEDSINGLE WAVELENGTHMx-ray1
2LIQUID NITROGEN COOLEDSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97631
21.00231
ReflectionResolution: 1.17→44.15 Å / Num. obs: 103174 / % possible obs: 91.2 % / Redundancy: 3.6 % / Biso Wilson estimate: 10.5 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 15.7
Reflection shellResolution: 1.17→1.21 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.6 / % possible all: 86.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XSCALEdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 1.17→44.15 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.203 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.14595 2782 2.7 %THIN SHELLS
Rwork0.11613 ---
obs0.11699 100391 91.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.611 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å20.11 Å2
2--0.43 Å20.28 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.17→44.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2715 0 7 441 3163
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022909
X-RAY DIFFRACTIONr_bond_other_d0.0010.022803
X-RAY DIFFRACTIONr_angle_refined_deg1.5491.9443960
X-RAY DIFFRACTIONr_angle_other_deg0.76436477
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0835349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.73424.407118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.65315530
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6921512
X-RAY DIFFRACTIONr_chiral_restr0.0950.2481
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213176
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02660
X-RAY DIFFRACTIONr_nbd_refined0.2510.2894
X-RAY DIFFRACTIONr_nbd_other0.1760.22659
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21462
X-RAY DIFFRACTIONr_nbtor_other0.0820.21511
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.298
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2750.269
X-RAY DIFFRACTIONr_symmetry_vdw_other0.140.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.981.581394
X-RAY DIFFRACTIONr_mcbond_other1.9731.5771392
X-RAY DIFFRACTIONr_mcangle_it2.3892.3731740
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0621.9751515
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.692.8222219
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.56335712
X-RAY DIFFRACTIONr_sphericity_free48.2055132
X-RAY DIFFRACTIONr_sphericity_bonded13.11355960
LS refinement shellResolution: 1.17→1.222 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.239 311 -
Rwork0.217 11648 -
obs--86.37 %

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