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- PDB-5fld: Crystal structure of raptor adenovirus 1 fibre head, beta-hairpin... -

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Basic information

Entry
Database: PDB / ID: 5fld
TitleCrystal structure of raptor adenovirus 1 fibre head, beta-hairpin deleted form
ComponentsFIBER PROTEIN
KeywordsCELL ADHESION
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 ADENOVIRUS A
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.7 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 23, 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 1.3Mar 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant / _entity_src_gen.pdbx_host_org_vector
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 / 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

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Assembly

Deposited unit
A: FIBER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8225
Polymers17,6801
Non-polymers1424
Water2,234124
1
A: FIBER PROTEIN
hetero molecules

A: FIBER PROTEIN
hetero molecules

A: FIBER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,46615
Polymers53,0413
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 area5940 Å2
ΔGint-182.5 kcal/mol
Surface area16890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.400, 81.400, 81.400
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-2116-

HOH

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Components

#1: Protein FIBER PROTEIN / ADENOVIRUS FIBRE


Mass: 17680.219 Da / Num. of mol.: 1 / Fragment: MUTANT FIBRE HEAD DOMAIN, UNP RESIDUES 324-464 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RAPTOR ADENOVIRUS A / Description: SEE SECONDARY REFERENCE / Plasmid: PET28A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F4MI11
#2: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE 359-NYGLRVVNGELQNTP-373 HAS BEEN REPLACED BY THE SEQUENCE EF, REMOVING A BETA-HAIRPIN ...THE SEQUENCE 359-NYGLRVVNGELQNTP-373 HAS BEEN REPLACED BY THE SEQUENCE EF, REMOVING A BETA-HAIRPIN THAT CONTACTED A NEIGHBOURING MONOMER

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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: 2.6 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1 M HEPES-NAOH PH 7.5, 20% (V/V) JEFFAMINE M-600

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 27, 2014
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: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.7→45 Å / Num. obs: 20075 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.02 / Net I/σ(I): 374.5
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 3.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
MOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.7→45 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.73 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.19834 994 5 %COPIED FROM NATIVE
Rwork0.17446 ---
obs0.17565 19065 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.084 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms972 0 4 124 1100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.019999
X-RAY DIFFRACTIONr_bond_other_d0.0010.02976
X-RAY DIFFRACTIONr_angle_refined_deg1.571.9671358
X-RAY DIFFRACTIONr_angle_other_deg0.85732254
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9915127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.53323.51437
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.93815179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.137154
X-RAY DIFFRACTIONr_chiral_restr0.0860.2169
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021087
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02219
X-RAY DIFFRACTIONr_nbd_refined0.2060.2422
X-RAY DIFFRACTIONr_nbd_other0.1510.21768
X-RAY DIFFRACTIONr_nbtor_refined0.1650.2946
X-RAY DIFFRACTIONr_nbtor_other0.0730.21140
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1040.268
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0450.24
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3490.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1580.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0890.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9553.552499
X-RAY DIFFRACTIONr_mcbond_other2.9543.541498
X-RAY DIFFRACTIONr_mcangle_it4.7495.295623
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.6964.062500
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.0875.914733
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: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 72 -
Rwork0.23 1372 -
obs--100 %

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