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- PDB-2vtw: Structure of the C-terminal head domain of the fowl adenovirus ty... -

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Basic information

Entry
Database: PDB / ID: 2vtw
TitleStructure of the C-terminal head domain of the fowl adenovirus type 1 short fibre
ComponentsFIBER PROTEIN 2
KeywordsVIRAL PROTEIN / CELO / ADENOVIRUS / FIBER PROTEIN / SHORT FIBRE HEAD
Function / homology
Function and homology information


adhesion receptor-mediated virion attachment to host cell / viral capsid / 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 / Avian adenovirus fibre, N-terminal / Avian adenovirus fibre, N-terminal / Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesFOWL ADENOVIRUS 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsElBakkouri, M. / Seiradake, E. / Cusack, S. / Ruigrok, R.W.H. / Schoehn, G.
CitationJournal: Virology / Year: 2008
Title: Structure of the C-Terminal Head Domain of the Fowl Adenovirus Type 1 Short Fibre.
Authors: El Bakkouri, M. / Seiradake, E. / Cusack, S. / Ruigrok, R.W.H. / Schoehn, G.
History
DepositionMay 16, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FIBER PROTEIN 2
B: FIBER PROTEIN 2
C: FIBER PROTEIN 2
D: FIBER PROTEIN 2
E: FIBER PROTEIN 2
F: FIBER PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,30818
Polymers131,1636
Non-polymers1,14512
Water21,2041177
1
A: FIBER PROTEIN 2
E: FIBER PROTEIN 2
F: FIBER PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1549
Polymers65,5813
Non-polymers5726
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-102.16 kcal/mol
Surface area21930 Å2
MethodPISA
2
B: FIBER PROTEIN 2
C: FIBER PROTEIN 2
D: FIBER PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1549
Polymers65,5813
Non-polymers5726
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6890 Å2
ΔGint-102.53 kcal/mol
Surface area21970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)235.750, 235.750, 61.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11E-2099-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A206 - 410
2114B206 - 410
3114C206 - 410
4114D206 - 410
5114E206 - 410
6114F206 - 410

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Components

#1: Protein
FIBER PROTEIN 2 /


Mass: 21860.486 Da / Num. of mol.: 6 / Fragment: RECEPTOR-BINDING DOMAIN RESIDUES 206-410
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) FOWL ADENOVIRUS 1 / Strain: CELO / PHELPS / Plasmid: PPROEX HTB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q64762
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1177 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.58 % / Description: NONE
Crystal growDetails: 0.1 M LITHIUM SULPHATE, 0.1 M TRI-SODIUM CITRATE AT PH 5.6 AND 12% W/V POLYETHYLENE GLYCOL (PEG) 4000

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→47.6 Å / Num. obs: 117179 / % possible obs: 99.8 % / Redundancy: 3.63 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 8.99
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.61 % / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 3.19 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
SHELXDphasing
SHARPphasing
REFMAC5.2.0019refinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2→47.57 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.453 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.214 5865 5 %RANDOM
Rwork0.175 ---
obs0.177 111098 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--0.07 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 2→47.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9216 0 62 1177 10455
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0229530
X-RAY DIFFRACTIONr_bond_other_d0.0010.026064
X-RAY DIFFRACTIONr_angle_refined_deg1.4871.9513088
X-RAY DIFFRACTIONr_angle_other_deg0.951314880
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.78351235
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.02724.225374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.241151338
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6581542
X-RAY DIFFRACTIONr_chiral_restr0.0950.21544
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210718
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021902
X-RAY DIFFRACTIONr_nbd_refined0.1960.21505
X-RAY DIFFRACTIONr_nbd_other0.2030.26395
X-RAY DIFFRACTIONr_nbtor_refined0.1760.24645
X-RAY DIFFRACTIONr_nbtor_other0.0830.24862
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2833
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.090.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2190.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.231
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0641.57877
X-RAY DIFFRACTIONr_mcbond_other0.1851.52454
X-RAY DIFFRACTIONr_mcangle_it1.278210130
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.87133842
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.794.52952
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 1516 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.350.5
2Bmedium positional0.290.5
3Cmedium positional0.310.5
4Dmedium positional0.30.5
5Emedium positional0.280.5
6Fmedium positional0.280.5
1Amedium thermal2.652
2Bmedium thermal2.12
3Cmedium thermal3.192
4Dmedium thermal1.422
5Emedium thermal2.272
6Fmedium thermal1.862
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 402 -
Rwork0.228 7938 -
obs--97.59 %

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