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

ID or keywords:

Entry

Database: PDB / ID: 8ofq

Title

Human adenovirus type 25 fiber-knob protein

Components

Fiber

Keywords

VIRAL 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 / host cell nucleus
Similarity search - Function

Biological species

Human adenovirus 25

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.6 Å

Authors

Rizkallah, P.J. / Parker, A.L. / Mundy, R.M. / Baker, A.T.

Funding support

United Kingdom, 2items

Citation

Journal: 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

Deposition	Mar 16, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 20, 2023	Provider: repository / Type: Initial release
Revision 1.1	Oct 11, 2023	Group: 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 1.2	May 8, 2024	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8ofq.cif.gz	614.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8ofq.ent.gz	510.5 KB	Display	PDB format
PDBx/mmJSON format	8ofq.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/of/8ofq ftp://data.pdbj.org/pub/pdb/validation_reports/of/8ofq	HTTPS FTP

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Related structure data

Related structure data	8ofpC 8ofrC 8ofsC 8oftC 8ofuC 8ofvC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#132 - Dec 2010 Adenovirus similarity (8)

Deposited unit

A: Fiber

B: Fiber

C: Fiber

D: Fiber

E: Fiber

F: Fiber

G: Fiber

H: Fiber

hetero molecules

171 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Fiber

B: Fiber

C: Fiber

hetero molecules

defined by author
Evidence: homology
63.9 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Fiber

E: Fiber

F: Fiber

hetero molecules

defined by author
64 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

G: Fiber

hetero molecules

G: Fiber

hetero molecules

G: Fiber

hetero molecules

defined by author
64.4 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

H: Fiber

defined by author
63.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	146
Space group name H-M	H3

Components on special symmetry positions

ID	Model	Components
1	1	G-401- SO4
2	1	G-401- SO4
3	1	G-659- HOH
4	1	G-673- HOH
5	1	H-534- HOH
6	1	H-538- HOH
7	1	H-545- HOH

Noncrystallographic symmetry (NCS)

NCS domain:
NCS ensembles :

#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 Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C₄H₁₀O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1230 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.29 Å³/Da / Density % sol: 46.25 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 17, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.6→82.62 Å / Num. obs: 198233 / % possible obs: 100 % / Redundancy: 5.8 % / B_iso Wilson estimate: 21.7 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.071 / R_pim(I) all: 0.045 / R_rim(I) all: 0.078 / Net I/σ(I): 11.2
Reflection shell	Resolution: 1.6→1.64 Å / Redundancy: 5.6 % / R_merge(I) obs: 1.284 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 14640 / CC_1/2: 0.484 / R_pim(I) all: 0.815 / R_rim(I) all: 1.418 / % possible all: 100

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	1.6 Å	82.61 Å
Translation	1.6 Å	82.61 Å

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
Aimless	0.7.4	data scaling
PHASER	2.8.3	phasing
PDB_EXTRACT	3.27	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.6→82.61 Å / Cor.coef. F_o:F_c: 0.971 / Cor.coef. F_o:F_c 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

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19791	9768	4.9 %	RANDOM
R_work	0.17217	-	-	-
obs	0.17342	188438	99.95 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 30.101 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.08 Å²	-0.04 Å²	0 Å²
2-	-	-0.08 Å²	0 Å²
3-	-	-	0.26 Å²

Refinement step

Cycle: 1 / Resolution: 1.6→82.61 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11576	0	26	1230	12832

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.012	12188
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	11406
X-RAY DIFFRACTION	r_angle_refined_deg	1.499	1.65	16629
X-RAY DIFFRACTION	r_angle_other_deg	1.361	1.586	26290
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.736	5	1489
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.083	24.57	604
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.77	15	2083
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	9.723	15	34
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	1638
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	14061
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	2919
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.606	1.705	5896
X-RAY DIFFRACTION	r_mcbond_other	1.606	1.705	5895
X-RAY DIFFRACTION	r_mcangle_it	2.807	2.542	7405
X-RAY DIFFRACTION	r_mcangle_other	2.807	2.542	7406
X-RAY DIFFRACTION	r_scbond_it	1.676	1.892	6292
X-RAY DIFFRACTION	r_scbond_other	1.676	1.893	6293
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.495	2.77	9225
X-RAY DIFFRACTION	r_long_range_B_refined	7.149	21.395	13921
X-RAY DIFFRACTION	r_long_range_B_other	7.107	20.68	13589
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

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

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	6039	0.08
1	2	B	6039	0.08
2	1	A	6064	0.08
2	2	C	6064	0.08
3	1	A	6050	0.09
3	2	D	6050	0.09
4	1	A	6035	0.09
4	2	E	6035	0.09
5	1	A	6059	0.08
5	2	F	6059	0.08
6	1	A	6046	0.09
6	2	G	6046	0.09
7	1	A	6063	0.08
7	2	H	6063	0.08
8	1	B	6163	0.07
8	2	C	6163	0.07
9	1	B	6202	0.07
9	2	D	6202	0.07
10	1	B	6162	0.08
10	2	E	6162	0.08
11	1	B	6157	0.07
11	2	F	6157	0.07
12	1	B	6117	0.08
12	2	G	6117	0.08
13	1	B	6163	0.08
13	2	H	6163	0.08
14	1	C	6155	0.07
14	2	D	6155	0.07
15	1	C	6168	0.07
15	2	E	6168	0.07
16	1	C	6125	0.07
16	2	F	6125	0.07
17	1	C	6143	0.07
17	2	G	6143	0.07
18	1	C	6112	0.09
18	2	H	6112	0.09
19	1	D	6085	0.09
19	2	E	6085	0.09
20	1	D	6080	0.08
20	2	F	6080	0.08
21	1	D	6096	0.08
21	2	G	6096	0.08
22	1	D	6062	0.09
22	2	H	6062	0.09
23	1	E	6103	0.08
23	2	F	6103	0.08
24	1	E	6081	0.09
24	2	G	6081	0.09
25	1	E	6130	0.07
25	2	H	6130	0.07
26	1	F	6163	0.08
26	2	G	6163	0.08
27	1	F	6177	0.08
27	2	H	6177	0.08
28	1	G	6147	0.1
28	2	H	6147	0.1

LS refinement shell

Resolution: 1.6→1.641 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.295	765	-
R_work	0.292	13805	-
obs	-	-	99.48 %

Refinement TLS params.

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

ID	L11 (°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)
1	1.6111	0.3916	-0.0995	3.2513	-0.8963	1.2583	0.0851	0.1467	-0.096	-0.1798	0.0007	0.1884	0.1233	-0.1362	-0.0857	0.0238	0.0051	-0.024	0.054	-0.0211	0.0325	-19.8357	36.1577	-2.84
2	2.8934	1.3248	1.0772	1.8918	0.6677	2.7005	0.0045	0.3177	-0.3443	-0.0949	-0.0139	-0.2228	0.1259	0.3005	0.0094	0.0464	0.0348	0.0328	0.0973	-0.0193	0.07	7.4296	32.1294	-3.858
3	2.0186	-0.9464	-0.4946	2.7203	1.1798	2.5389	-0.0544	-0.2139	-0.2764	0.2026	-0.001	-0.0003	0.4329	0.0116	0.0554	0.1063	-0.0029	-0.0058	0.0413	0.0404	0.0512	-6.6209	26.0332	19.1167
4	1.238	0.8691	-0.7522	2.7679	-1.2312	2.5005	0.0151	-0.0809	0.0798	0.294	-0.042	0.3035	-0.1634	-0.1599	0.0269	0.0638	-0.0018	0.0401	0.0592	-0.0391	0.0592	-41.4697	71.2937	41.6684
5	2.8668	-0.9523	-1.3743	1.6916	0.2895	2.4827	0.0345	0.2552	-0.0898	-0.1985	-0.1026	0.31	0.1464	-0.4602	0.0681	0.0609	-0.0321	-0.0351	0.1234	-0.0395	0.071	-44.1181	56.1002	18.7587
6	3.5288	0.6487	0.8039	1.7793	0.4333	1.4587	0.0355	-0.1938	-0.3995	0.2058	0.0361	0.067	0.3345	-0.0897	-0.0716	0.1172	-0.0138	0.0211	0.0421	0.0162	0.0836	-31.7018	45.4672	41.0382
7	1.9801	-0.2004	-1.3136	1.3788	0.753	2.7052	-0.0397	-0.0443	-0.2307	0.1977	0.0075	0.0437	0.2447	-0.0392	0.0322	0.0501	-0.0086	-0.0058	0.0057	0.012	0.0387	-2.6159	57.3644	63.4284
8	2.2164	0.2071	1.1856	1.7229	0.7034	2.8436	-0.0945	0.2055	0.3001	-0.3014	0.0873	-0.0293	-0.2508	0.0126	0.0072	0.1074	-0.0067	0.0137	0.0458	0.0406	0.0554	1.8315	15.8483	58.2169

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	{ A\|186-371 }	A	186 - 371
2	X-RAY DIFFRACTION	2	{ B\|186-371 }	B	186 - 371
3	X-RAY DIFFRACTION	3	{ C\|186-371 }	C	186 - 371
4	X-RAY DIFFRACTION	4	{ D\|186-371 }	D	186 - 371
5	X-RAY DIFFRACTION	5	{ E\|186-371 }	E	186 - 371
6	X-RAY DIFFRACTION	6	{ F\|186-371 }	F	186 - 371
7	X-RAY DIFFRACTION	7	{ G\|186-371 }	G	186 - 371
8	X-RAY DIFFRACTION	8	{ H\|186-371 }	H	186 - 371

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