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

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Basic information

Entry
Database: PDB / ID: 4umi
TitleCrystal structure of the fiber head domain of the Atadenovirus snake adenovirus 1, native, F23 crystal form
ComponentsFIBER PROTEIN
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


viral capsid / cell adhesion / symbiont entry into host cell / host cell nucleus / virion attachment to host cell
Similarity search - Function
: / Atadenovirus fibre, head domain / Adenovirus fibre protein / Attachment protein shaft domain superfamily
Similarity search - Domain/homology
Biological speciesSNAKE ADENOVIRUS 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 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 17, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 25, 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 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FIBER PROTEIN


Theoretical massNumber of molelcules
Total (without water)22,1421
Polymers22,1421
Non-polymers00
Water2,720151
1
A: FIBER PROTEIN

A: FIBER PROTEIN

A: FIBER PROTEIN


Theoretical massNumber of molelcules
Total (without water)66,4263
Polymers66,4263
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_554z,x+1/2,y-1/21
crystal symmetry operation45_455y-1/2,z+1/2,x1
Buried area5380 Å2
ΔGint-26.9 kcal/mol
Surface area14870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.520, 121.520, 121.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23
Components on special symmetry positions
IDModelComponents
11A-2003-

HOH

21A-2005-

HOH

31A-2006-

HOH

41A-2007-

HOH

51A-2008-

HOH

61A-2009-

HOH

71A-2124-

HOH

81A-2125-

HOH

91A-2147-

HOH

101A-2148-

HOH

111A-2150-

HOH

121A-2151-

HOH

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Components

#1: Protein FIBER PROTEIN / SPIKE / PROTEIN IV


Mass: 22141.865 Da / Num. of mol.: 1 / Fragment: FIBER HEAD PLUS SHAFT DOMAIN, RESIDUES 171-339
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, I.E. ADDITIONAL REFERENCE 2.
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A9CB96
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsC-TERMINAL PART OF SEQUENCE IS DIFFERENT, WE THINK BECAUSE THE DATABASE 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: 1.7 Å3/Da / Density % sol: 27 % / 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: Diamond / Beamline: I02 / Wavelength: 0.9797
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 3, 2013
Details: KIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSSING
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.826
11K, H, -L20.174
ReflectionResolution: 1.33→43 Å / Num. obs: 33985 / % possible obs: 99.5 % / Redundancy: 5.8 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.5
Reflection shellResolution: 1.33→1.36 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.2 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4D0V CHAIN A

4d0v


Resolution: 1.33→42.96 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.717 / SU ML: 0.015 / Cross valid method: THROUGHOUT / ESU R: 0.007 / ESU R Free: 0.007 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.13804 1832 5.4 %RANDOM
Rwork0.11733 ---
obs0.11848 32152 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.225 Å2
Baniso -1Baniso -2Baniso -3
1--1.74 Å22.47 Å2-5.69 Å2
2---2.73 Å2-2.36 Å2
3---4.47 Å2
Refinement stepCycle: LAST / Resolution: 1.33→42.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms859 0 0 151 1010
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.019891
X-RAY DIFFRACTIONr_bond_other_d0.0010.02844
X-RAY DIFFRACTIONr_angle_refined_deg1.6141.9911212
X-RAY DIFFRACTIONr_angle_other_deg0.81331966
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4855117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.16823.93933
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.2215144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.548154
X-RAY DIFFRACTIONr_chiral_restr0.1160.2138
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021995
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02187
X-RAY DIFFRACTIONr_nbd_refined0.2520.2224
X-RAY DIFFRACTIONr_nbd_other0.1920.2754
X-RAY DIFFRACTIONr_nbtor_refined0.1860.2421
X-RAY DIFFRACTIONr_nbtor_other0.0880.2473
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.219
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0370.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3470.245
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1630.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3570.29
X-RAY DIFFRACTIONr_symmetry_hbond_other0.2090.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8641.858459
X-RAY DIFFRACTIONr_mcbond_other1.887458
X-RAY DIFFRACTIONr_mcangle_it2.3562.79573
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4272.293432
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8653.28638
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr5.2793891
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded11.2355868
LS refinement shellResolution: 1.33→1.365 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 138 -
Rwork0.21 2285 -
obs--95.17 %

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