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- PDB-6stt: Adenovirus 29 Fiber Knob protein in complex with Sialic acid -

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Basic information

Entry
Database: PDB / ID: 6stt
TitleAdenovirus 29 Fiber Knob protein in complex with Sialic acid
ComponentsFiber
KeywordsVIRAL PROTEIN / Adenovirus / Type 29 / Sialic Acid / 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 / host cell nucleus
Similarity search - Function
Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein, knob / Adenoviral fibre protein (knob domain) / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein / Attachment protein shaft domain superfamily / Adenovirus pIV-like, attachment domain
Similarity search - Domain/homology
N-acetyl-alpha-neuraminic acid / Fiber
Similarity search - Component
Biological speciesHuman adenovirus 29
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.54 Å
AuthorsBaker, A.T. / Mundy, R.M. / 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 / database_2
Item: _citation.pdbx_database_id_DOI / _citation.year ..._citation.pdbx_database_id_DOI / _citation.year / _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)42,6124
Polymers41,9932
Non-polymers6192
Water6,666370
1
A: Fiber
hetero molecules

A: Fiber
hetero molecules

A: Fiber
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9186
Polymers62,9903
Non-polymers9283
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area7840 Å2
ΔGint-37 kcal/mol
Surface area21400 Å2
MethodPISA
2
B: Fiber
hetero molecules

B: Fiber
hetero molecules

B: Fiber
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9186
Polymers62,9903
Non-polymers9283
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_454-z-1,x,-y-11
crystal symmetry operation11_544y,-z-1,-x-11
Buried area7910 Å2
ΔGint-36 kcal/mol
Surface area21970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.236, 104.236, 104.236
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-665-

HOH

21B-658-

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: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 47.36 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M SPG Buffer, 25% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.54→60.25 Å / Num. obs: 55982 / % possible obs: 100 % / Redundancy: 22.4 % / CC1/2: 1 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.02 / Rrim(I) all: 0.096 / Net I/σ(I): 17.9
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
1.54-1.5722.32.376227627870.6050.5122.4251.4100
8.44-60.1818.70.03737839410.0070.0317799.7

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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: 1.54→60.25 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.971 / SU B: 3.999 / SU ML: 0.061 / SU R Cruickshank DPI: 0.0818 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.073
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1878 2767 4.9 %RANDOM
Rwork0.1398 ---
obs0.1423 53165 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 121.88 Å2 / Biso mean: 27.295 Å2 / Biso min: 15.28 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.54→60.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2852 0 42 370 3264
Biso mean--59.2 38.48 -
Num. residues----356
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132983
X-RAY DIFFRACTIONr_bond_other_d0.0040.0172698
X-RAY DIFFRACTIONr_angle_refined_deg1.6681.6494064
X-RAY DIFFRACTIONr_angle_other_deg1.4331.5766319
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.815358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.53325.524143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.75515509
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.171154
X-RAY DIFFRACTIONr_chiral_restr0.080.2421
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023280
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02568
X-RAY DIFFRACTIONr_rigid_bond_restr4.36232983
LS refinement shellResolution: 1.54→1.58 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 206 -
Rwork0.263 3880 -
all-4086 -
obs--99.98 %
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)
12.3589-1.03040.48371.8114-0.35581.45270.05980.12450.217-0.1255-0.0916-0.3564-0.12730.01620.03180.03110.00770.03420.00780.01940.0761-19.1678-17.7965-37.8687
21.8015-1.00790.38722.3546-0.52231.4539-0.0928-0.12810.35350.10930.0656-0.2122-0.00940.12910.02720.0070.0082-0.01890.0319-0.03520.0753-17.783-19.174-66.3991
30.0035-0.0180.01080.9426-0.46480.23230.0042-0.0354-0.0087-0.2301-0.00410.01720.1362-0.0265-0.00010.3832-0.03120.03320.4573-0.03740.3029-33.5891-33.6237-52.0852
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A187 - 371
2X-RAY DIFFRACTION2B187 - 371
3X-RAY DIFFRACTION3A - B400 - 401

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