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- PDB-8ofq: Human adenovirus type 25 fiber-knob protein -

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Basic information

Entry
Database: PDB / ID: 8ofq
TitleHuman adenovirus type 25 fiber-knob protein
ComponentsFiber
KeywordsVIRAL PROTEIN / Adenovirus / Fiber knob / Ad25
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
DI(HYDROXYETHYL)ETHER / Fiber
Similarity search - Component
Biological speciesHuman adenovirus 25
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsRizkallah, P.J. / Parker, A.L. / Mundy, R.M. / Baker, A.T.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N0137941/1 United Kingdom
Wellcome Trust517732 United Kingdom
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
DepositionMar 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 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
Revision 1.2May 8, 2024Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_PubMed / _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
C: Fiber
D: Fiber
E: Fiber
F: Fiber
G: Fiber
H: Fiber
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,70413
Polymers170,2478
Non-polymers4565
Water22,1581230
1
A: Fiber
B: Fiber
C: Fiber
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9394
Polymers63,8433
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-31 kcal/mol
Surface area21980 Å2
2
D: Fiber
E: Fiber
F: Fiber
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0015
Polymers63,8433
Non-polymers1582
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-31 kcal/mol
Surface area21580 Å2
3
G: Fiber
hetero molecules

G: Fiber
hetero molecules

G: Fiber
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4499
Polymers63,8433
Non-polymers6076
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area6540 Å2
ΔGint-67 kcal/mol
Surface area22200 Å2
4
H: Fiber

H: Fiber

H: Fiber


Theoretical massNumber of molelcules
Total (without water)63,8433
Polymers63,8433
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area5500 Å2
ΔGint-25 kcal/mol
Surface area21940 Å2
Unit cell
Length a, b, c (Å)126.552, 126.552, 251.444
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11G-401-

SO4

21G-401-

SO4

31G-659-

HOH

41G-673-

HOH

51H-534-

HOH

61H-538-

HOH

71H-545-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
77
88
99
1010
1111
1212
1313
1414
1515
1616
1717
1818
1919
2020
2121
2222
2323
2424
2525
2626
2727
2828

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

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Components

#1: Protein
Fiber /


Mass: 21280.912 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 25 / Strain: 25 / Gene: L5 / Production host: Escherichia coli (E. coli) / References: UniProt: M0QUM1
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1230 / 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: 2.29 Å3/Da / Density % sol: 46.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M SPG buffer, 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: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6→82.62 Å / Num. obs: 198233 / % possible obs: 100 % / Redundancy: 5.8 % / Biso Wilson estimate: 21.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.045 / Rrim(I) all: 0.078 / Net I/σ(I): 11.2
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 5.6 % / Rmerge(I) obs: 1.284 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 14640 / CC1/2: 0.484 / Rpim(I) all: 0.815 / Rrim(I) all: 1.418 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.6 Å82.61 Å
Translation1.6 Å82.61 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→82.61 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 4.011 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19791 9768 4.9 %RANDOM
Rwork0.17217 ---
obs0.17342 188438 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.101 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0.04 Å20 Å2
2---0.08 Å20 Å2
3---0.26 Å2
Refinement stepCycle: 1 / Resolution: 1.6→82.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11576 0 26 1230 12832
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01212188
X-RAY DIFFRACTIONr_bond_other_d0.0010.01511406
X-RAY DIFFRACTIONr_angle_refined_deg1.4991.6516629
X-RAY DIFFRACTIONr_angle_other_deg1.3611.58626290
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.73651489
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.08324.57604
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.77152083
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.7231534
X-RAY DIFFRACTIONr_chiral_restr0.0810.21638
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214061
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022919
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6061.7055896
X-RAY DIFFRACTIONr_mcbond_other1.6061.7055895
X-RAY DIFFRACTIONr_mcangle_it2.8072.5427405
X-RAY DIFFRACTIONr_mcangle_other2.8072.5427406
X-RAY DIFFRACTIONr_scbond_it1.6761.8926292
X-RAY DIFFRACTIONr_scbond_other1.6761.8936293
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4952.779225
X-RAY DIFFRACTIONr_long_range_B_refined7.14921.39513921
X-RAY DIFFRACTIONr_long_range_B_other7.10720.6813589
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A60390.08
12B60390.08
21A60640.08
22C60640.08
31A60500.09
32D60500.09
41A60350.09
42E60350.09
51A60590.08
52F60590.08
61A60460.09
62G60460.09
71A60630.08
72H60630.08
81B61630.07
82C61630.07
91B62020.07
92D62020.07
101B61620.08
102E61620.08
111B61570.07
112F61570.07
121B61170.08
122G61170.08
131B61630.08
132H61630.08
141C61550.07
142D61550.07
151C61680.07
152E61680.07
161C61250.07
162F61250.07
171C61430.07
172G61430.07
181C61120.09
182H61120.09
191D60850.09
192E60850.09
201D60800.08
202F60800.08
211D60960.08
212G60960.08
221D60620.09
222H60620.09
231E61030.08
232F61030.08
241E60810.09
242G60810.09
251E61300.07
252H61300.07
261F61630.08
262G61630.08
271F61770.08
272H61770.08
281G61470.1
282H61470.1
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 765 -
Rwork0.292 13805 -
obs--99.48 %
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)
11.61110.3916-0.09953.2513-0.89631.25830.08510.1467-0.096-0.17980.00070.18840.1233-0.1362-0.08570.02380.0051-0.0240.054-0.02110.0325-19.835736.1577-2.84
22.89341.32481.07721.89180.66772.70050.00450.3177-0.3443-0.0949-0.0139-0.22280.12590.30050.00940.04640.03480.03280.0973-0.01930.077.429632.1294-3.858
32.0186-0.9464-0.49462.72031.17982.5389-0.0544-0.2139-0.27640.2026-0.001-0.00030.43290.01160.05540.1063-0.0029-0.00580.04130.04040.0512-6.620926.033219.1167
41.2380.8691-0.75222.7679-1.23122.50050.0151-0.08090.07980.294-0.0420.3035-0.1634-0.15990.02690.0638-0.00180.04010.0592-0.03910.0592-41.469771.293741.6684
52.8668-0.9523-1.37431.69160.28952.48270.03450.2552-0.0898-0.1985-0.10260.310.1464-0.46020.06810.0609-0.0321-0.03510.1234-0.03950.071-44.118156.100218.7587
63.52880.64870.80391.77930.43331.45870.0355-0.1938-0.39950.20580.03610.0670.3345-0.0897-0.07160.1172-0.01380.02110.04210.01620.0836-31.701845.467241.0382
71.9801-0.2004-1.31361.37880.7532.7052-0.0397-0.0443-0.23070.19770.00750.04370.2447-0.03920.03220.0501-0.0086-0.00580.00570.0120.0387-2.615957.364463.4284
82.21640.20711.18561.72290.70342.8436-0.09450.20550.3001-0.30140.0873-0.0293-0.25080.01260.00720.1074-0.00670.01370.04580.04060.05541.831515.848358.2169
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|186-371 }A186 - 371
2X-RAY DIFFRACTION2{ B|186-371 }B186 - 371
3X-RAY DIFFRACTION3{ C|186-371 }C186 - 371
4X-RAY DIFFRACTION4{ D|186-371 }D186 - 371
5X-RAY DIFFRACTION5{ E|186-371 }E186 - 371
6X-RAY DIFFRACTION6{ F|186-371 }F186 - 371
7X-RAY DIFFRACTION7{ G|186-371 }G186 - 371
8X-RAY DIFFRACTION8{ H|186-371 }H186 - 371

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