PDB-4xqb: CRYSTAL STRUCTURE OF AD37 FIBER KNOB IN COMPLEX WITH TRIVALENT SI...

ID or keywords:

Entry

Database: PDB / ID: 4xqb

Title

CRYSTAL STRUCTURE OF AD37 FIBER KNOB IN COMPLEX WITH TRIVALENT SIALIC ACID INHIBITOR ME0461

Components

Fiber

Keywords

VIRAL PROTEIN / ADENOVIRUS / FIBER KNOB / PROTEIN CARBOHYDRATE INTERACTION / SIALIC ACID / CARBOHYDRATE MIMIC / MULTIVALENT LIGAND

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 / metal ion binding
Similarity search - Function

Biological species

Human adenovirus 37

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.597 Å

Authors

Stehle, T. / Liaci, A.M.

Funding support

Germany,

Sweden, 6items

Organization	Grant number	Country
German Research Foundation	SFB 685	Germany
Swedish Research Council	521-2010-3078	Sweden
Swedish Research Council	621-2010-4746	Sweden
Knut and Alice Wallenberg Foundation	2009.0009	Sweden
Stiftelsen foer Strategisk Forskning	F06-0011	Sweden
Torsten Soederbergs Stiftelse	M4/11	Sweden

Citation

Journal: Org.Biomol.Chem. / Year: 2015
Title: Triazole linker-based trivalent sialic acid inhibitors of adenovirus type 37 infection of human corneal epithelial cells.
Authors: Caraballo, R. / Saleeb, M. / Bauer, J. / Liaci, A.M. / Chandra, N. / Storm, R.J. / Frangsmyr, L. / Qian, W. / Stehle, T. / Arnberg, N. / Elofsson, M.

History

Deposition	Jan 19, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Jul 29, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 2, 2015	Group: Database references
Revision 2.0	Sep 6, 2017	Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Derived calculations Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_site_gen Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.ptnr2_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1	Jun 12, 2019	Group: Data collection / Structure summary Category: audit_author / database_PDB_rev / database_PDB_rev_record Item: _audit_author.name
Revision 2.2	Jan 10, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4xqb.cif.gz	247.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4xqb.ent.gz	196.7 KB	Display	PDB format
PDBx/mmJSON format	4xqb.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4xqb_validation.pdf.gz	962.2 KB	Display	wwPDB validaton report
Full document	4xqb_full_validation.pdf.gz	966.4 KB	Display
Data in XML	4xqb_validation.xml.gz	29.9 KB	Display
Data in CIF	4xqb_validation.cif.gz	44.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xq/4xqb ftp://data.pdbj.org/pub/pdb/validation_reports/xq/4xqb	HTTPS FTP

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Related structure data

Related structure data	4k6tC 4k6uC 4k6vC 4k6wC 4xqaC 1uxeS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3qnd-1 6qpm-2 3n0i-d 1uxe-d 4k6v-d 4k6t-2 4k6t-1 2wgu-d 3qnd-2 2wgt-d Search similar-shape structures by Omokage search (details) 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

hetero molecules

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

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	61.440, 70.320, 74.480
Angle α, β, γ (deg.)	90.000, 94.470, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Fiber / Fiber protein Mass: 21716.535 Da / Num. of mol.: 3 / Fragment: UNP residues 177-365 Source method: isolated from a genetically manipulated source Details: FRAGMENT: FIBER KNOB / Source: (gene. exp.) Human adenovirus 37 / Gene: L5 / Plasmid: PPROEX HTB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q64823
#2: Chemical	ChemComp-425 / 2-(1-{2-[bis(2-{4-[2-({(6R)-5-(acetylamino)-3,5-dideoxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]-beta-L-threo-hex-2-ulopyranonosyl}oxy)ethyl]-1H-1,2,3-triazol-1-yl}ethyl)amino]ethyl}-1H-1,2,3-triazol-4-yl)ethyl (6R)-5-(acetylamino)-3,5-dideoxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]-beta-L-threo-hex-2-ulopyranosidonic acid Mass: 1308.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₅₁H₈₁N₁₃O₂₇
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 654 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.57 Å³/Da / Density % sol: 52.18 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9 / Details: 28% PEG 8000, 0.1M HEPES, 0.05M zinc acetate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2014
Radiation	Monochromator: Si111-DCM with sagital bender / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 1.597→50 Å / Num. obs: 83280 / % possible obs: 99.4 % / Redundancy: 3.73 % / R_merge(I) obs: 0.066 / Net I/σ(I): 14.9
Reflection shell	Resolution: 1.597→1.69 Å / Redundancy: 3.57 % / R_merge(I) obs: 0.656 / Mean I/σ(I) obs: 2 / % possible all: 97.2

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Processing

Software

Name	Version	Classification
PHENIX		refinement
PDB_EXTRACT	3.15	data extraction
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1uxe

1uxe

Resolution: 1.597→45.541 Å / FOM work R set: 0.8978 / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.54 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1784	4164	5 %
R_work	0.1569	79114	-
obs	0.158	83278	99.37 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 100.72 Å² / B_iso mean: 21.13 Å² / B_iso min: 6.15 Å²

Refinement step

Cycle: final / Resolution: 1.597→45.541 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4354	0	123	654	5131
B_iso mean	-	-	22.57	30.44	-
Num. residues	-	-	-	-	553

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	4632
X-RAY DIFFRACTION	f_angle_d	1.227	6322
X-RAY DIFFRACTION	f_chiral_restr	0.087	726
X-RAY DIFFRACTION	f_plane_restr	0.006	795
X-RAY DIFFRACTION	f_dihedral_angle_d	11.503	1695

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.5974-1.6156	0.2864	120	0.2657	2295	2415	87
1.6156-1.6346	0.2589	140	0.2352	2636	2776	100
1.6346-1.6545	0.2345	137	0.2273	2637	2774	100
1.6545-1.6755	0.2457	139	0.2106	2630	2769	100
1.6755-1.6975	0.2317	139	0.2098	2635	2774	100
1.6975-1.7208	0.2396	138	0.2088	2616	2754	100
1.7208-1.7454	0.2048	139	0.1945	2647	2786	100
1.7454-1.7714	0.2232	140	0.1934	2653	2793	100
1.7714-1.7991	0.2379	140	0.1907	2658	2798	100
1.7991-1.8286	0.2413	139	0.1743	2635	2774	100
1.8286-1.8601	0.2097	138	0.174	2646	2784	100
1.8601-1.894	0.2016	138	0.1721	2631	2769	100
1.894-1.9304	0.2323	139	0.1731	2636	2775	100
1.9304-1.9698	0.1905	139	0.1701	2641	2780	100
1.9698-2.0126	0.2216	140	0.1651	2645	2785	100
2.0126-2.0594	0.1842	138	0.1551	2615	2753	100
2.0594-2.1109	0.1859	140	0.1513	2674	2814	100
2.1109-2.168	0.1649	139	0.1475	2633	2772	100
2.168-2.2318	0.1655	138	0.1461	2636	2774	100
2.2318-2.3038	0.1781	140	0.1471	2639	2779	100
2.3038-2.3862	0.1589	141	0.1596	2683	2824	100
2.3862-2.4817	0.165	138	0.1496	2641	2779	99
2.4817-2.5946	0.2059	140	0.1527	2644	2784	100
2.5946-2.7314	0.1668	139	0.1529	2643	2782	100
2.7314-2.9025	0.1669	141	0.1546	2677	2818	100
2.9025-3.1266	0.1661	139	0.1499	2652	2791	100
3.1266-3.4411	0.1707	141	0.1493	2662	2803	100
3.4411-3.9388	0.1706	139	0.1475	2655	2794	99
3.9388-4.9615	0.1298	142	0.1204	2688	2830	100
4.9615-45.5596	0.1586	144	0.1565	2731	2875	100

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	0.0636	0.0454	0.0654	0.1226	0.1096	0.0955	-0.1248	0.0152	-0.372	-0.0929	-0.0276	-0.3277	-0.002	0.0166	0.0003	0.1492	0.0683	0.0588	0.1782	0.0735	0.312	-0.0368	-6.7309	-28.9169
2	0.0074	0.0054	0.0104	0.0335	-0.0135	0.1212	0.0081	0.0368	-0.1213	-0.1327	-0.0088	-0.1966	0.0369	0.1455	0.0179	0.1506	0.0352	0.0569	0.1352	0.0279	0.1624	-4.637	-3.4406	-35.1672
3	0.6458	0.275	-0.0102	0.2118	0.0591	0.304	-0.1006	0.0988	-0.13	-0.1375	0.013	-0.1923	0.1463	0.0381	-0.0351	0.1449	0.0355	0.073	0.1069	0.0013	0.1583	-7.0846	-4.4432	-35.869
4	0.4901	0.259	-0.1555	0.1531	-0.1267	0.3392	-0.0445	0.0748	-0.0457	-0.1178	-0.0233	-0.0893	0.1388	0.0277	-0.0871	0.1177	0.0097	0.019	0.0587	0.0013	0.0864	-16.8214	-3.7278	-31.9718
5	0.0215	0.01	-0.0059	0.0007	0.005	0.0247	-0.0052	-0.2429	-0.0398	0.1517	-0.1064	-0.0371	0.035	0.2923	-0	0.2167	0.0043	-0.0459	0.2844	0.0179	0.156	-7.9491	3.1112	-0.7098
6	0.3738	0.1609	-0.2141	0.1294	-0.1311	0.4406	0.0179	-0.2751	-0.0295	0.0858	-0.2335	-0.167	-0.038	0.3493	-0.1913	0.1484	-0.0794	-0.0829	0.2187	-0.0379	0.1188	-8.538	11.0971	-4.1015
7	0.1009	0.0485	0.0187	0.0461	-0.0511	0.1338	0.0231	-0.1173	0.0599	-0.121	-0.0687	-0.123	-0.1936	0.1406	-0.0242	0.1503	-0.0106	-0.0249	0.1273	-0.0318	0.1266	-12.8956	11.8939	-8.5175
8	0.3129	0.0739	-0.2971	0.073	-0.0133	0.707	0.2142	-0.1834	0.1941	0.0365	-0.0992	-0.0666	-0.4623	0.4151	0.1261	0.1248	-0.0591	-0.0464	0.2298	-0.0277	0.2015	-5.4025	17.9145	-10.0803
9	0.0003	0.004	0.0165	0.0029	0.0005	0.0003	-0.021	-0.3595	0.1735	0.0265	0.0592	-0.0433	0.0403	0.1932	0.0001	0.1636	-0.0003	-0.0746	0.3618	-0.0186	0.1427	-2.0716	6.9505	-0.7747
10	0.0695	-0.0959	-0.0169	0.1259	0.0259	0.0248	0.059	-0.0942	0.0423	0.1318	0.0375	-0.2543	0.0792	-0.0206	0.0556	0.1325	0.0064	-0.2232	0.6679	0.1743	0.1421	-0.0565	-0.6952	2.1854
11	0.1598	0.0997	0.1574	0.3996	-0.0302	0.6417	-0.0071	-0.05	0.0577	0.037	-0.0777	-0.1032	-0.0996	0.1074	-0.0871	0.0607	-0.0024	-0.0097	0.1097	0.0134	0.1362	-8.5516	11.0645	-17.2552
12	0.0445	-0.0209	0.0001	0.038	0.0569	0.1276	-0.1022	-0.0562	-0.1698	0.1618	0.0042	-0.0003	0.2786	-0.0194	-0.0159	0.1693	0.0162	-0.0007	0.1067	0.0216	0.1313	-25.3941	-17.1208	-15.8649
13	0.0326	0.0628	-0.0443	0.1525	-0.0338	0.1264	-0.0426	-0.0584	-0.0342	0.0186	-0.0129	0.023	0.1095	-0.0058	-0.0264	0.0882	0.0079	-0.0024	0.0964	0.0026	0.0845	-30.4505	-8.7512	-17.2676
14	0.1877	0.1947	-0.058	0.2095	0.0436	0.0473	0.0084	-0.0537	0.0111	0.1377	-0.048	0.0817	0.0055	-0.0298	-0.0145	0.1288	0.0073	-0.0081	0.1353	0.0155	0.0996	-36.6711	-5.2548	-10.8449
15	0.2158	0.0746	-0.1472	0.0886	-0.0854	0.1343	-0.0714	-0.0962	-0.1029	0.0046	0.0319	0.0135	0.2762	0.1118	-0.0046	0.2475	0.0155	-0.0269	0.1348	0.0455	0.1174	-23.6486	-17.7037	-7.4255
16	0.4397	0.268	-0.1898	0.3745	-0.0651	0.0723	0.0255	-0.0717	0.0189	0.0442	-0.009	0.0655	-0.0183	0.018	0.0158	0.0908	0.0135	-0.0066	0.0963	-0.0084	0.0612	-28.5071	1.1791	-13.7566

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 182 through 197 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 198 through 213 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 214 through 280 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 281 through 365 )	A
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 181 through 197 )	B
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 198 through 213 )	B
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 214 through 234 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 235 through 260 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 261 through 270 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 271 through 283 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 284 through 365 )	B
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 182 through 197 )	C
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 198 through 234 )	C
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 235 through 263 )	C
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 264 through 291 )	C
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 292 through 365 )	C

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