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- PDB-5fjl: Crystal structure of raptor adenovirus 1 fibre head, wild-type form -

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Basic information

Entry
Database: PDB / ID: 5fjl
TitleCrystal structure of raptor adenovirus 1 fibre head, wild-type form
ComponentsFIBER PROTEINFibrous protein
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
Similarity search - Function
Avian adenovirus fibre, N-terminal / Avian adenovirus fibre, N-terminal / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein / Attachment protein shaft domain superfamily
Similarity search - Domain/homology
Biological speciesRAPTOR SIADENOVIRUS A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsNguyen, T.H. / van Raaij, M.J.
Citation
Journal: Virol.J. / Year: 2016
Title: Crystal Structure of Raptor Adenovirus 1 Fibre Head and Role of the Beta-Hairpin in Siadenovirus Fibre Head Domains
Authors: Nguyen, T.H. / Ballmann, M.Z. / Do, H.T. / Truong, H.N. / Benko, M. / Harrach, B. / van Raaij, M.J.
#1: Journal: Infect.Genet.Evol / Year: 2011
Title: Complete Sequence of Raptor Adenovirus 1 Confirms the Characteristic Genome Organization of Siadenoviruses.
Authors: Kovacs, E.R. / Benko, M.
History
DepositionOct 9, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Database references
Revision 1.2Dec 13, 2017Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2035
Polymers19,0611
Non-polymers1424
Water3,135174
1
A: FIBER PROTEIN
hetero molecules

A: FIBER PROTEIN
hetero molecules

A: FIBER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,60815
Polymers57,1823
Non-polymers42512
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_545-y,z-1/2,-x+1/21
crystal symmetry operation7_555-z+1/2,-x,y+1/21
Buried area8080 Å2
ΔGint-186.4 kcal/mol
Surface area16530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.720, 81.720, 81.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-2165-

HOH

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Components

#1: Protein FIBER PROTEIN / Fibrous protein / ADENOVIRUS FIBRE


Mass: 19060.756 Da / Num. of mol.: 1 / Fragment: FIBRE HEAD DOMAIN, RESIDUES 324-464
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RAPTOR SIADENOVIRUS A / Description: SEE SECONDARY REFERENCE / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: F4MI11
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsNCBI REFERENCE SEQUENCE YP_004414817.1

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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: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growpH: 9
Details: 20 MM BICINE-NAOH PH 9.0, 50 MM MAGNESIUM CHLORIDE, 5 MM L-ARGININE, 5% (V/V) GLYCEROL, 1.5 M SODIUM CHLORIDE, 10% (V/V) ETHANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97952
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 17, 2013
Details: VERTICAL FOCUSING MIRROR AND HORIZONTAL FOCUSING MIRROR ORTHOGONAL IN A KIRKPATRICK-BAEZ CONFIGURATION
RadiationMonochromator: CRYOGENICALLY COOLED CHANNEL-CUT DCM SI (111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97952 Å / Relative weight: 1
ReflectionResolution: 1.47→47.2 Å / Num. obs: 31365 / % possible obs: 100 % / Redundancy: 9.9 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 29.6
Reflection shellResolution: 1.47→1.49 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZPE

3zpe


Resolution: 1.47→45 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.93 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.17862 1586 5.1 %RANDOM
Rwork0.15682 ---
obs0.1579 29748 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.629 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.47→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1069 0 4 174 1247
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191154
X-RAY DIFFRACTIONr_bond_other_d0.0020.021149
X-RAY DIFFRACTIONr_angle_refined_deg1.6611.9751586
X-RAY DIFFRACTIONr_angle_other_deg0.92832658
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1215155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.81223.72143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.22915209
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.864155
X-RAY DIFFRACTIONr_chiral_restr0.1040.2201
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021283
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02256
X-RAY DIFFRACTIONr_nbd_refined0.2040.2590
X-RAY DIFFRACTIONr_nbd_other0.1560.21944
X-RAY DIFFRACTIONr_nbtor_refined0.170.21060
X-RAY DIFFRACTIONr_nbtor_other0.0730.21276
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.268
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2450.241
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1710.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0680.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6112.132571
X-RAY DIFFRACTIONr_mcbond_other1.5842.129570
X-RAY DIFFRACTIONr_mcangle_it2.4793.196719
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7892.49582
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.3123.605858
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: 1.468→1.506 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 127 -
Rwork0.222 2179 -
obs--100 %

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