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- PDB-4d0v: Crystal structure of the fiber head domain of the Atadenovirus sn... -

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Basic information

Entry
Database: PDB / ID: 4d0v
TitleCrystal structure of the fiber head domain of the Atadenovirus snake adenovirus 1, native, I213 crystal form
ComponentsFIBER PROTEIN
KeywordsVIRAL PROTEIN
Function / homologyAdenovirus fibre protein / Attachment protein shaft domain superfamily / viral capsid / cell adhesion / symbiont entry into host cell / host cell nucleus / virion attachment to host cell / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / Fiber protein
Function and homology information
Biological speciesSNAKE ADENOVIRUS 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.7 Å
AuthorsSingh, A.K. / van Raaij, M.J.
Citation
Journal: PLoS ONE / Year: 2014
Title: Crystal structure of the fibre head domain of the Atadenovirus Snake Adenovirus 1.
Authors: Singh, A.K. / Menendez-Conejero, R. / San Martin, C. / van Raaij, M.J.
#1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2013
Title: Crystallization of the C-terminal domain of the fibre protein from snake adenovirus 1, an atadenovirus.
Authors: Singh, A.K. / Menendez-Conejero, R. / San Martin, C. / van Raaij, M.J.
#2: Journal: Archives of Virology / Year: 1993
Title: Physicochemical Properties and Cytopathogenicity of an Adenovirus-Like Agent Isolated from Corn Snake (Elaphe Guttata).
Authors: Juhasz, A. / Ahne, W.
#3: Journal: Virus Res. / Year: 2008
Title: Completion of the Genome Analysis of Snake Adenovirus Type 1, a Representative of the Reptilian Lineage within the Novel Genus Atadenovirus.
Authors: Farkas, S.L. / Harrach, B. / Benko, M.
History
DepositionApr 30, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 4, 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.title / _citation_author.name
Revision 1.3May 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
B: FIBER PROTEIN
C: FIBER PROTEIN
D: FIBER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9109
Polymers61,8814
Non-polymers1,0295
Water10,305572
1
A: FIBER PROTEIN
B: FIBER PROTEIN
C: FIBER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4408
Polymers46,4113
Non-polymers1,0295
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-45.8 kcal/mol
Surface area13620 Å2
MethodPISA
2
D: FIBER PROTEIN

D: FIBER PROTEIN

D: FIBER PROTEIN


Theoretical massNumber of molelcules
Total (without water)46,4113
Polymers46,4113
Non-polymers00
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 area4220 Å2
ΔGint-19.6 kcal/mol
Surface area17080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.620, 149.620, 149.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11B-1345-

SO4

21B-2113-

HOH

31D-2011-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.361, 0.37126, -0.85548), (0.4757, 0.86233, 0.17349), (0.80211, -0.34432, -0.48791)68.30987, -15.115, 98.70263
2given(-0.36516, 0.48662, 0.79364), (0.37676, 0.85682, -0.352), (-0.8513, 0.17047, -0.49622)-46.88158, 22.30255, 109.87769
3given(0.85602, 0.35166, 0.37889), (-0.17695, -0.48934, 0.85395), (0.48571, -0.79804, -0.35666)-24.25676, -65.93497, 89.24128
4given(-0.36786, 0.38276, -0.84745), (0.4824, 0.85768, 0.17798), (0.79497, -0.34334, -0.50014)67.60844, -15.36266, 99.69485
5given(-0.48691, 0.78621, 0.38052), (-0.85875, -0.35131, -0.37299), (-0.15957, -0.50838, 0.84622)-15.88972, 23.70355, 9.28427
6given(0.15761, 0.5079, -0.84688), (0.49797, -0.78145, -0.37598), (-0.85275, -0.36246, -0.37608)65.69008, 15.50312, 98.85374

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Components

#1: Protein
FIBER PROTEIN / SPIKE / PROTEIN IV / FIBER PROTEIN OF THE ATADENOVIRUS SNAKE ADENOVIRUS 1


Mass: 15470.341 Da / Num. of mol.: 4 / Fragment: FIBER HEAD DOMAIN, RESIDUES 234-339
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SNAKE ADENOVIRUS 1
Description: SNAKE ADENOVIRUS 1 (SNADV1) WAS FIRST ISOLATED FROM THE CORN SNAKE ELAPHE GUTTATA, JUHASZ & AHNE, 1993, SEE ADDITIONAL REFERENCE 2.
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A9CB96
#2: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H34O9
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 572 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE C-TERMINAL PART OF THE SEQUENCE IS DIFFERENT, WE BELIEVE THE DATABASE SEQUENCE IS WRONG.

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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: 2.3 Å3/Da / Density % sol: 46 % / Description: NONE
Crystal growpH: 7.5
Details: 10 MM TRIS-HCL, 1.7 M AMMONIUM SULFATE, 0.085 M HEPES SODIUM SALT PH 7.5, 1.7%(V/V) POLYETHYLENE GLYCOL (PEG) 400, 15%(V/V) GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 10, 2012 / Details: VERTICALLY BENDED MULTILAYER MIRRORS
RadiationMonochromator: DIAMOND (001) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 60984 / % possible obs: 99.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.3
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 7.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.98 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20125 1604 2.6 %THIN SHELLS COPIED FROM DERIVATIVE DATA
Rwork0.16704 ---
obs0.168 59326 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.083 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3286 0 65 572 3923
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223506
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.9964741
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.175441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.74523.525139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.87315575
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4771521
X-RAY DIFFRACTIONr_chiral_restr0.0990.2538
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212581
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.21479
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22338
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2423
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.293
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.256
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9031.52185
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.64723521
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.48331321
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.324.51216
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→1.803 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.239 233 -
Rwork0.226 9523 -
obs--99.93 %

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