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- PDB-4d0u: Crystal structure of the fiber head domain of the Atadenovirus sn... -

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Basic information

Entry
Database: PDB / ID: 4d0u
TitleCrystal structure of the fiber head domain of the Atadenovirus snake adenovirus 1, selenomethionine-derivative
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 / MAD / Resolution: 1.6 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 1.2Apr 29, 2015Group: Data collection
Revision 1.3Jan 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 2.0Dec 19, 2018Group: Atomic model / Data collection / Derived calculations
Category: atom_site / struct_conn / Item: _atom_site.label_alt_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)63,68810
Polymers62,5634
Non-polymers1,1256
Water9,620534
1
A: FIBER PROTEIN
B: FIBER PROTEIN
C: FIBER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6778
Polymers46,9223
Non-polymers7555
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-40.5 kcal/mol
Surface area13660 Å2
MethodPISA
2
D: FIBER PROTEIN
hetero molecules

D: FIBER PROTEIN
hetero molecules

D: FIBER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0336
Polymers46,9223
Non-polymers1,1113
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 area4190 Å2
ΔGint-21.7 kcal/mol
Surface area13900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.540, 149.540, 149.540
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-1346-

SO4

31B-1346-

SO4

41B-2054-

HOH

51B-2121-

HOH

61C-2116-

HOH

71D-2018-

HOH

81D-2112-

HOH

91D-2137-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.36934, 0.36594, -0.85421), (0.46967, 0.86667, 0.1682), (0.80187, -0.33908, -0.49197)68.53525, -14.77436, 98.75262
2given(-0.36896, 0.48796, 0.79105), (0.37773, 0.85637, -0.35207), (-0.84922, 0.16891, -0.50029)-0.31009, 0.14867, 0.73649
3given(0.85437, 0.36224, 0.3726), (-0.16615, -0.48896, 0.85634), (0.49238, -0.79354, -0.35757)-23.87586, -66.36921, 88.99033
4given(-0.36241, 0.38169, -0.85028), (0.47332, 0.86127, 0.18488), (0.80289, -0.33545, -0.49279)67.99879, -15.89412, 98.7602
5given(-0.49403, 0.78253, 0.37892), (-0.85407, -0.3552, -0.38), (-0.16277, -0.51135, 0.84382)-0.10372, 0.16201, 0.06348
6given(0.155, 0.51, -0.846), (0.496, -0.781, -0.379), (-0.854, -0.361, -0.374)0.43859, 0.10367, 0.66067

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Components

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


Mass: 15640.671 Da / Num. of mol.: 4 / Fragment: FIBER HEAD DOMAIN, RESIDUES 234-339 / Mutation: YES
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, I.E. ADDITIONAL REFERENCE 2.
Plasmid: PET28C / 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.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 534 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsLEU322 AND LEU324 WERE MUTATED TO MET. THE C-TERMINAL PART OF THE SEQUENCE IS DIFFERENT, WE BELIEVE ...LEU322 AND LEU324 WERE MUTATED TO MET. THE 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: 2.24 Å3/Da / Density % sol: 45.24 % / Description: NONE
Crystal growpH: 7.5
Details: 10 MM TRIS-HCL PH 8.5, 10 MM BETA-MERCAPTOETHANOL, 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: ID14-4 / Wavelength: 0.9768, 0.9791, 0.9793
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 26, 2012 / Details: TOROIDAL FOCUSING MIRROR
RadiationMonochromator: CHANNEL CUT ESRF MONOCHROMATOR SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97681
20.97911
30.97931
ReflectionResolution: 1.6→30 Å / Num. obs: 72960 / % possible obs: 100 % / Redundancy: 12.2 % / Biso Wilson estimate: 13.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 18.2
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 6.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
MOSFLMdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.6→29.33 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.324 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.18854 1975 2.7 %THIN SHELLS
Rwork0.15797 ---
obs0.15884 70937 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.448 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3228 0 70 534 3832
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193465
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5421.9984684
X-RAY DIFFRACTIONr_angle_other_deg
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_restr0.1030.2528
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212556
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2250.22009
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22338
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2158
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2480.2149
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3361.4051737
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.2012.0952175
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4421.7491728
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9352.4772503
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→1.697 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.192 392 -
Rwork0.19 11269 -
obs--99.97 %

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