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- PDB-2ium: Structure of the C-terminal head domain of the avian adenovirus C... -

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Basic information

Entry
Database: PDB / ID: 2ium
TitleStructure of the C-terminal head domain of the avian adenovirus CELO long fibre (C2 crystal form)
ComponentsAVIAN ADENOVIRUS CELO LONG FIBRE
KeywordsVIRAL PROTEIN / RECEPTOR-BINDING / AVIAN ADENOVIRUS / TRIMERIC PROTEINS / VIRAL FIBRES / BETA-SANDWICH / FIBER PROTEIN
Function / homology
Function and homology information


adhesion receptor-mediated virion attachment to host cell / viral capsid / symbiont entry into host cell / host cell nucleus
Similarity search - Function
Fiber protein 1, C-terminal domain / Fiber protein 1, C-terminal / Fiber protein, C-terminal domain superfamily / C-terminal head domain of the fowl adenovirus type 1 long fibre / Avian adenovirus fibre, N-terminal / Avian adenovirus fibre, N-terminal / Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein (repeat/shaft region) / Attachment protein shaft domain superfamily ...Fiber protein 1, C-terminal domain / Fiber protein 1, C-terminal / Fiber protein, C-terminal domain superfamily / C-terminal head domain of the fowl adenovirus type 1 long fibre / Avian adenovirus fibre, N-terminal / Avian adenovirus fibre, N-terminal / Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein (repeat/shaft region) / Attachment protein shaft domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fiber protein 1 / Long fiber
Similarity search - Component
Biological speciesAVIAN ADENOVIRUS GAL1
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.6 Å
AuthorsGuardado-Calvo, P. / Llamas-Saiz, A.L. / Fox, G.C. / van Raaij, M.J.
Citation
Journal: J. Gen. Virol. / Year: 2007
Title: Structure of the C-terminal head domain of the fowl adenovirus type 1 long fiber.
Authors: Guardado-Calvo, P. / Llamas-Saiz, A.L. / Fox, G.C. / Langlois, P. / van Raaij, M.J.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Crystallization of the C-Terminal Head Domain of the Avian Adenovirus Celo Long Fibre
Authors: Guardado-Calvo, P. / Llamas-Saiz, A.L. / Langlois, P. / van Raaij, M.J.
#2: Journal: J.Virol. / Year: 1996
Title: The Complete DNA Sequence and Genomic Organization of the Avian Adenovirus Celo.
Authors: Chiocca, S. / Kurzbauer, R. / Schaffner, G. / Baker, A. / Mautner, V. / Cotten, M.
#3: Journal: J.Mol.Biol. / Year: 1995
Title: The Avian Adenovirus Penton: Two Fibres and One Base.
Authors: Hess, M. / Cuzange, A. / Ruigrok, R.W. / Chroboczek, J. / Jacrot, B.
History
DepositionJun 6, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2018Group: Database references / Refinement description / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / software
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name / _software.name
Revision 1.4May 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 / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AVIAN ADENOVIRUS CELO LONG FIBRE
B: AVIAN ADENOVIRUS CELO LONG FIBRE
C: AVIAN ADENOVIRUS CELO LONG FIBRE


Theoretical massNumber of molelcules
Total (without water)79,4603
Polymers79,4603
Non-polymers00
Water15,439857
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6790 Å2
ΔGint-36.6 kcal/mol
Surface area28660 Å2
MethodPQS
Unit cell
Length a, b, c (Å)216.836, 58.649, 57.591
Angle α, β, γ (deg.)90.00, 101.50, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2078-

HOH

21B-2136-

HOH

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Components

#1: Protein AVIAN ADENOVIRUS CELO LONG FIBRE


Mass: 26486.662 Da / Num. of mol.: 3 / Fragment: C-TERMINAL HEAD DOMAIN, RESIDUES 579-793
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AVIAN ADENOVIRUS GAL1 / Strain: TYPE 1 / Plasmid: PET28C-PLUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 / Variant (production host): DE3 / References: UniProt: Q64787, UniProt: Q64761*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 857 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCRYSTALLISED SEQUENCE CONTAINS N-TERMINAL PURIFICATION TAG

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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: 2.65 Å3/Da / Density % sol: 53.5 %
Description: THE FILE R2IUMSF.ENT CONTAINS DETAILS OF THE MIR DATASETS USED FOR DETERMINING THE STRUCTURE.
Crystal growpH: 5.5
Details: 10-12% PEG 10000; 0.1 M HEPES-HAOH PH 4.7-6.1; 0-10% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.97986
DetectorType: MARRESEARCH MAR165 / Detector: CCD / Date: Feb 25, 2006 / Details: FLAT AND TOROIDAL MIRROR
RadiationMonochromator: DOUBLE SI(111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97986 Å / Relative weight: 1
ReflectionResolution: 1.6→25 Å / Num. obs: 88294 / % possible obs: 93.8 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.9
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.3 / % possible all: 73

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXDEphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.6→16 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.814 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 2034 2.3 %SHELLS
Rwork0.18 ---
obs0.18 85836 94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.91 Å2
Baniso -1Baniso -2Baniso -3
1--1.38 Å20 Å2-0.29 Å2
2--3.15 Å20 Å2
3----1.88 Å2
Refinement stepCycle: LAST / Resolution: 1.6→16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4797 0 0 857 5654
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224935
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6181.966771
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5285630
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.21324.677186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.08115702
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.91159
X-RAY DIFFRACTIONr_chiral_restr0.1060.2777
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023777
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.22363
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.23444
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2689
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1370.228
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1290.242
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.46423223
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.08135145
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.46831975
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.34851626
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: 1.6→1.69 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.306 230
Rwork0.31 9941

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