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- PDB-6stv: Adenovirus 29 Fiber Knob protein -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6stv
TitleAdenovirus 29 Fiber Knob protein
ComponentsFiber
KeywordsVIRAL PROTEIN / Adenovirus / Type 29 / 3D Structure / Fiber Knob
Function / homology
Function and homology information


adhesion receptor-mediated virion attachment to host cell / viral capsid / cell adhesion / symbiont entry into host cell
Similarity search - Function
Adenoviral fibre protein, knob / Adenoviral fibre protein (knob domain) / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein / Attachment protein shaft domain superfamily / Adenovirus pIV-like, attachment domain
Similarity search - Domain/homology
PHOSPHATE ION / Fiber
Similarity search - Component
Biological speciesHuman adenovirus 29
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsMundy, R.M. / Baker, A.T. / Rizkallah, P.J. / Parker, A.L.
CitationJournal: npj Viruses / Year: 2023
Title: Broad sialic acid usage amongst species D human adenovirus
Authors: Mundy, R.M. / Baker, A.T. / Bates, E.A. / Cunliffe, T.G. / Teijeira-Crespo, A. / Moses, E. / Rizkallah, P.J. / Parker, A.L.
History
DepositionSep 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2
Item: _citation.pdbx_database_id_DOI / _citation.title ..._citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fiber
B: Fiber
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2755
Polymers41,9932
Non-polymers2823
Water5,999333
1
A: Fiber
hetero molecules

A: Fiber
hetero molecules

A: Fiber
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5519
Polymers62,9903
Non-polymers5616
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation12_555-y,-z,x1
Buried area7400 Å2
ΔGint-43 kcal/mol
Surface area22370 Å2
MethodPISA
2
B: Fiber
hetero molecules

B: Fiber
hetero molecules

B: Fiber
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2756
Polymers62,9903
Non-polymers2853
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_656-z+1,-x,y+11
crystal symmetry operation10_546-y,z-1,-x+11
Buried area6880 Å2
ΔGint-44 kcal/mol
Surface area22140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.290, 104.290, 104.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number195
Space group name H-MP23
Components on special symmetry positions
IDModelComponents
11A-401-

PO4

21A-401-

PO4

31B-401-

PO4

41B-401-

PO4

51A-654-

HOH

61B-654-

HOH

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Components

#1: Protein Fiber


Mass: 20996.715 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 29 / Gene: L5 / Production host: Escherichia coli (E. coli) / References: UniProt: E1CIQ3
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.34 Å3/Da / Density % sol: 47.44 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1M SPG, 25% w/v PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER2 X 500K / Detector: PIXEL / Date: Apr 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.6→73.85 Å / Num. obs: 50042 / % possible obs: 100 % / Redundancy: 22.6 % / CC1/2: 1 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.023 / Rrim(I) all: 0.109 / Net I/σ(I): 18.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.6-1.6322.53.6035493924470.4440.7763.6861100
8.76-73.7420.10.024714135510.0060.02598.299.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→73.85 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / SU B: 4.533 / SU ML: 0.075 / SU R Cruickshank DPI: 0.0882 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.085
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2006 2470 4.9 %RANDOM
Rwork0.1768 ---
obs0.178 47543 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 116.45 Å2 / Biso mean: 30.003 Å2 / Biso min: 17.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.6→73.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2852 0 16 333 3201
Biso mean--43.31 38.67 -
Num. residues----356
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132977
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172710
X-RAY DIFFRACTIONr_angle_refined_deg1.6991.6424057
X-RAY DIFFRACTIONr_angle_other_deg1.4031.5756340
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.325364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.90425.714140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.04615512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.55154
X-RAY DIFFRACTIONr_chiral_restr0.0840.2412
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023296
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02572
LS refinement shellResolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 151 -
Rwork0.317 3515 -
all-3666 -
obs--99.95 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.67480.99850.66852.02720.45691.8060.0704-0.1210.18060.1485-0.09420.3578-0.1436-0.01030.02380.0337-0.00920.03650.0074-0.01720.069719.1689-17.777937.8835
21.95420.98390.40252.59610.61741.7416-0.090.14740.3532-0.11370.0710.1778-0.0114-0.1410.0190.0067-0.0091-0.01720.03340.03690.070717.7794-19.167166.4069
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 184
2X-RAY DIFFRACTION2B0 - 184

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