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- PDB-7x5t: Structure of the C-terminal head domain of the fowl adenovirus ty... -

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Basic information

Entry
Database: PDB / ID: 7x5t
TitleStructure of the C-terminal head domain of the fowl adenovirus type 4 fiber 1
ComponentsFiber-1
KeywordsVIRAL PROTEIN / fiber / receptor binding
Function / homologyFiber protein 1, C-terminal / Fiber protein, C-terminal domain superfamily / C-terminal head domain of the fowl adenovirus type 1 long fibre / Avian adenovirus fibre, N-terminal / Avian adenovirus fibre, N-terminal / virion attachment to host cell / Fiber-1
Function and homology information
Biological speciesFowl adenovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSong, Y.P. / Wei, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of the C-terminal head domain of the fowl adenovirus type 4 fiber 1
Authors: Song, Y.P. / Wei, Q.
History
DepositionMar 5, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fiber-1


Theoretical massNumber of molelcules
Total (without water)27,2641
Polymers27,2641
Non-polymers00
Water3,873215
1
A: Fiber-1

A: Fiber-1

A: Fiber-1


Theoretical massNumber of molelcules
Total (without water)81,7923
Polymers81,7923
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation12_555-y,-z,x1
Buried area5840 Å2
ΔGint-44 kcal/mol
Surface area23660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.600, 116.600, 116.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number207
Space group name H-MP432
Components on special symmetry positions
IDModelComponents
11A-344-

HOH

21A-449-

HOH

31A-473-

HOH

41A-498-

HOH

51A-505-

HOH

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Components

#1: Protein Fiber-1 /


Mass: 27264.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fowl adenovirus / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2Z4HVS3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.42 Å3/Da / Density % sol: 49.23 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 0.1M Na citrate tribasic dihydrate pH5.0, 30% PEG monomethyl ether 550

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Data collection

DiffractionMean temperature: 273 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM02 / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.65→47.65 Å / Num. obs: 33187 / % possible obs: 100 % / Redundancy: 75.7 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 27.1
Reflection shellResolution: 1.65→1.68 Å / Rmerge(I) obs: 3.295 / Num. unique obs: 1575

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IUN

2iun


Resolution: 1.65→47.65 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.672 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1897 1650 5 %RANDOM
Rwork0.1352 ---
obs0.1379 31537 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.1 Å2 / Biso mean: 30.582 Å2 / Biso min: 18.72 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.65→47.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 0 215 1844
Biso mean---42.04 -
Num. residues----216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0121751
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171582
X-RAY DIFFRACTIONr_angle_refined_deg1.4111.6472425
X-RAY DIFFRACTIONr_angle_other_deg1.2831.5613670
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7125236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.32724.475
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.47515247
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.413154
X-RAY DIFFRACTIONr_chiral_restr0.0620.2242
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022055
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02397
X-RAY DIFFRACTIONr_rigid_bond_restr1.57333332
LS refinement shellResolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 120 -
Rwork0.206 2273 -
all-2393 -
obs--100 %

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