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- PDB-6itx: Structure of the C-terminal head domain of the avian adenovirus E... -

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Basic information

Entry
Database: PDB / ID: 6itx
TitleStructure of the C-terminal head domain of the avian adenovirus EDSV fiber
ComponentsFiber protein
KeywordsCELL ADHESION / avian adenovirus / fiber protein
Function / homology
Function and homology information


adhesion receptor-mediated virion attachment to host cell / virion component / cell adhesion / symbiont entry into host cell / host cell nucleus
Similarity search - Function
Fiber protein 1, C-terminal domain / Fiber protein 1, C-terminal / Fiber protein, C-terminal domain superfamily / C-terminal head domain of the fowl adenovirus type 1 long fibre / Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein / Attachment protein shaft domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
GLUTAMINE / Fiber protein / Fiber protein
Similarity search - Component
Biological speciesDuck adenovirus 1
MethodX-RAY DIFFRACTION / Resolution: 2.75 Å
AuthorsWei, Q. / Song, Y.
Funding support China, 1items
OrganizationGrant numberCountry
China
CitationJournal: Int.J.Biol.Macromol. / Year: 2019
Title: Unravelling the receptor binding property of egg drop syndrome virus (EDSV) from the crystal structure of EDSV fiber head.
Authors: Song, Y. / Wei, Q. / Liu, Y. / Feng, H. / Chen, Y. / Wang, Y. / Bai, Y. / Xing, G. / Deng, R. / Zhang, G.
History
DepositionNov 26, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fiber protein
B: Fiber protein
D: Fiber protein
C: Fiber protein
E: Fiber protein
F: Fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,81716
Polymers192,6066
Non-polymers1,21110
Water4,594255
1
A: Fiber protein
B: Fiber protein
C: Fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7877
Polymers96,3033
Non-polymers4844
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-69 kcal/mol
Surface area24750 Å2
MethodPISA
2
D: Fiber protein
E: Fiber protein
F: Fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,0299
Polymers96,3033
Non-polymers7276
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7090 Å2
ΔGint-94 kcal/mol
Surface area25450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.515, 63.236, 165.806
Angle α, β, γ (deg.)90.000, 93.540, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Fiber protein / EDSV fiber


Mass: 32100.943 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Duck adenovirus 1 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: S4TZM6, UniProt: O11424*PLUS
#2: Chemical
ChemComp-GLN / GLUTAMINE


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C5H10N2O3
#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.: 255 / Source method: isolated from a natural source / Formula: H2O

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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: 2.86 Å3/Da / Density % sol: 56.92 %
Crystal growTemperature: 293.15 K / Method: evaporation / Details: 0.2M Potassium sulfate, 15% w/v PEG 3350

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Data collection

DiffractionMean temperature: 285 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: May 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.75→30 Å / Num. obs: 57643 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 46.9 Å2 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.051 / Rrim(I) all: 0.131 / Χ2: 0.99 / Net I/σ(I): 5.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.75-2.85.70.47328300.8990.2150.5210.96399.6
2.8-2.855.90.41428240.9310.1840.4540.97599.4
2.85-2.96.40.39928800.9440.1690.4340.99699.6
2.9-2.966.70.37428260.9560.1560.4060.95599.6

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
AMoREphasing
RefinementResolution: 2.75→29.882 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.28
RfactorNum. reflection% reflection
Rfree0.2316 2902 5.08 %
Rwork0.1922 --
obs0.1943 57130 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 122.8 Å2 / Biso mean: 46.6149 Å2 / Biso min: 13.64 Å2
Refinement stepCycle: final / Resolution: 2.75→29.882 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9920 0 70 255 10245
Biso mean--64.16 41.91 -
Num. residues----1313
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810272
X-RAY DIFFRACTIONf_angle_d1.00314086
X-RAY DIFFRACTIONf_chiral_restr0.0551599
X-RAY DIFFRACTIONf_plane_restr0.0071816
X-RAY DIFFRACTIONf_dihedral_angle_d13.4085866
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7377-2.78250.34121010.23362015211678
2.7825-2.83050.29281340.2242419255394
2.8305-2.88190.28721230.21962557268097
2.8819-2.93730.31211270.22782610273799
2.9373-2.99720.29751450.23482585273099
2.9972-3.06230.26021550.224725542709100
3.0623-3.13340.27161500.211726182768100
3.1334-3.21170.24161500.197225642714100
3.2117-3.29850.23181370.196626492786100
3.2985-3.39540.25711170.197325922709100
3.3954-3.50480.25721330.18842635276899
3.5048-3.62990.23491390.19092570270999
3.6299-3.77490.21551310.182126402771100
3.7749-3.94640.22571580.177726442802100
3.9464-4.15390.21440.169825802724100
4.1539-4.41340.15271380.156926372775100
4.4134-4.75290.20821330.158626382771100
4.7529-5.22890.1871600.161326252785100
5.2289-5.98030.23291490.186626492798100
5.9803-7.51470.26481290.209326912820100
7.5147-29.8840.24151490.231727562905100

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