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- PDB-4d1g: Crystal structure of the fiber head domain of the Atadenovirus sn... -

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Basic information

Entry
Database: PDB / ID: 4d1g
TitleCrystal structure of the fiber head domain of the Atadenovirus snake adenovirus 1, native, second P212121 crystal form
ComponentsFIBER PROTEIN
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


viral capsid / cell adhesion / symbiont entry into host cell / virion attachment to host cell / host cell nucleus
Similarity search - Function
: / Atadenovirus fibre, head domain / Adenovirus fibre protein / Attachment protein shaft domain superfamily
Similarity search - Domain/homology
3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / Fiber protein
Similarity search - Component
Biological speciesSNAKE ADENOVIRUS 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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: Arch.Virol. / 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
DepositionMay 1, 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 1.3Dec 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

Downloads & links

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Assembly

Deposited unit
A: FIBER PROTEIN
B: FIBER PROTEIN
C: FIBER PROTEIN
D: FIBER PROTEIN
E: FIBER PROTEIN
F: FIBER PROTEIN
G: FIBER PROTEIN
H: FIBER PROTEIN
I: FIBER PROTEIN
J: FIBER PROTEIN
K: FIBER PROTEIN
L: FIBER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,14423
Polymers184,44112
Non-polymers2,70311
Water15,979887
1
D: FIBER PROTEIN
E: FIBER PROTEIN
F: FIBER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2064
Polymers46,1103
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-44.9 kcal/mol
Surface area13340 Å2
MethodPISA
2
G: FIBER PROTEIN
H: FIBER PROTEIN
I: FIBER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6736
Polymers46,1103
Non-polymers5633
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-27 kcal/mol
Surface area13530 Å2
MethodPISA
3
J: FIBER PROTEIN
K: FIBER PROTEIN
L: FIBER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2226
Polymers46,1103
Non-polymers1,1113
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-35 kcal/mol
Surface area13540 Å2
MethodPISA
4
A: FIBER PROTEIN
B: FIBER PROTEIN
C: FIBER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0437
Polymers46,1103
Non-polymers9334
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-29 kcal/mol
Surface area13530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.770, 96.750, 153.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 15370.116 Da / Num. of mol.: 12 / 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.: 6 / Source method: obtained synthetically / Formula: C16H34O9
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 887 / 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: 1.8 Å3/Da / Density % sol: 31 % / 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) PEG 400, 15%(V/V) GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9999
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 7, 2012
Details: CYLINDRICAL GRAZING INCIDENCE MIRROR BENT TO APPROXIMATE TO A TOROIDAL CURVATURE
RadiationMonochromator: LIQUID NITROGEN COOLED CHANNEL-CUT SILICON MONOCHROMATOR, SI(111) AND SI (311)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.9→70 Å / Num. obs: 113650 / % possible obs: 99.9 % / Redundancy: 11.9 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.6
Reflection shellResolution: 1.9→2 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 6.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4D0V

4d0v


Resolution: 1.9→29.73 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.7 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23945 2003 1.8 %THIN SHELLS
Rwork0.17314 ---
obs0.17437 111478 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: 32.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.69 Å20 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9718 0 175 887 10780
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02210303
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3851.99213938
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.21751321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.73323.815401
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.923151683
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8181552
X-RAY DIFFRACTIONr_chiral_restr0.0950.21587
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217604
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.190.24295
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.27008
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2778
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.265
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2130.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.31726462
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.609410391
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.44283841
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it9.324123528
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: 1.9→2.031 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.25 278 -
Rwork0.212 19922 -
obs--99.89 %

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