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- PDB-4cw8: Structure of the carboxy-terminal domain of the turkey type 3 sia... -

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Basic information

Entry
Database: PDB / ID: 4cw8
TitleStructure of the carboxy-terminal domain of the turkey type 3 siadenovirus fibre, virulent form
ComponentsFIBER KNOB DOMAIN
KeywordsVIRAL PROTEIN / BETA-SANDWICH
Function / homologyAdenovirus Type 5 Fiber Protein (Receptor Binding Domain) - #50 / Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) / Sandwich / Mainly Beta / PHOSPHATE ION / Fiber knob domain
Function and homology information
Biological speciesTURKEY ADENOVIRUS 3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
DepositionApr 1, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2015Provider: 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 1.3Dec 20, 2023Group: 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

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Assembly

Deposited unit
A: FIBER KNOB DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0253
Polymers20,8351
Non-polymers1902
Water72140
1
A: FIBER KNOB DOMAIN
hetero molecules

A: FIBER KNOB DOMAIN
hetero molecules

A: FIBER KNOB DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0759
Polymers62,5053
Non-polymers5706
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation5_555z,x,y1
Buried area8110 Å2
ΔGint-74.3 kcal/mol
Surface area16600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.963, 98.963, 98.963
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-2001-

HOH

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Components

#1: Protein FIBER KNOB DOMAIN / TURKEY ADENOVIRUS TYPE 3 FIBRE


Mass: 20835.156 Da / Num. of mol.: 1 / Fragment: HEAD DOMAIN, RESIDUES 12-165 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TURKEY ADENOVIRUS 3 / Strain: AVIRULENT HEMORRHAGIC ENTERITIS VACCINE, LIVE VIRUS / Description: ARKO LABORATORIES, JEWELL IA / Variant: VETERINARY LICENSE NO. 337, SERIAL NO. 2081 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q0GF90
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL HIS-TAG, METHIONINE 354 WAS MUTATED TO ISOLEUCINE AND METHIONINE 376 WAS MUTATED TO ...N-TERMINAL HIS-TAG, METHIONINE 354 WAS MUTATED TO ISOLEUCINE AND METHIONINE 376 WAS MUTATED TO THREONINE TO MAKE THE SEQUENCE CONFORM TO THE VIRULENT VERSION

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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: 2.1 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growpH: 7
Details: 10MM [2-(N-MORPHOLINO)ETHANESULFONIC ACID]-NAOH PH 6.0, 1M (NH4)2HPO4, 0.1 M IMIDAZOLE PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97946
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 26, 2013
Details: PAIR OF KB MIRRORS FOR ADJUSTABLE FOCUSING, PLANE- ELLIPSOIDAL, THREE COATING STRIPES (SI, RH, IR) - IRELEC INSYNC
RadiationMonochromator: CHANNEL-CUT DOUBLE CRYSTAL MONOCHROMATOR (CINEL), CRYOCOOLED, 6MM GAP
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.3→31.3 Å / Num. obs: 7327 / % possible obs: 100 % / Redundancy: 8.9 % / Biso Wilson estimate: 56.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 6.3
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 1.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZPE

3zpe


Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.934 / SU B: 9.997 / SU ML: 0.231 / Cross valid method: THROUGHOUT / ESU R: 0.318 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23888 334 4.6 %RANDOM
Rwork0.19694 ---
obs0.19903 6962 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.861 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1091 0 10 40 1141
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191120
X-RAY DIFFRACTIONr_bond_other_d0.0010.021125
X-RAY DIFFRACTIONr_angle_refined_deg1.5531.9761522
X-RAY DIFFRACTIONr_angle_other_deg0.76132576
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.080.2180
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211242
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02255
X-RAY DIFFRACTIONr_nbd_refined0.2080.2174
X-RAY DIFFRACTIONr_nbd_other0.1790.21107
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2516
X-RAY DIFFRACTIONr_nbtor_other0.0840.2690
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.229
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1340.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1710.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1060.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.0986.162551
X-RAY DIFFRACTIONr_mcbond_other5.0896.147550
X-RAY DIFFRACTIONr_mcangle_it7.3259.206687
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.5286.819569
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.4719.982835
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: 2.301→2.424 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.321 40 -
Rwork0.245 984 -
obs--99.9 %

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