PDB-3hg0: Crystal structure of a DARPin in complex with ORF49 from Lactococ...

ID or keywords:

Entry

Database: PDB / ID: 3hg0

Title

Crystal structure of a DARPin in complex with ORF49 from Lactococcal phage TP901-1

Components

Baseplate protein
Designed Ankyrin Repeat Protein (DARPin) 20

Keywords

PROTEIN BINDING

Function / homology

Function and homology information

virus tail, baseplate / cell adhesion / virion attachment to host cell
Similarity search - Function

Biological species

Lactococcus phage TP901-1 (virus)
artificial gene (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Veesler, D. / Dreier, B. / Blangy, S. / Lichiere, J. / Tremblay, D. / Moineau, S. / Spinelli, S. / Tegoni, M. / Pluckthun, A. / Campanacci, V. / Cambillau, C.

Citation

Journal: J.Biol.Chem. / Year: 2009
Title: Crystal structure and function of a DARPin neutralizing inhibitor of lactococcal phage TP901-1: comparison of DARPin and camelid VHH binding mode.
Authors: Veesler, D. / Dreier, B. / Blangy, S. / Lichiere, J. / Tremblay, D. / Moineau, S. / Spinelli, S. / Tegoni, M. / Pluckthun, A. / Campanacci, V. / Cambillau, C.

History

Deposition	May 13, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 8, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Sep 25, 2013	Group: Derived calculations
Revision 1.3	Sep 6, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3hg0.cif.gz	220.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3hg0.ent.gz	179 KB	Display	PDB format
PDBx/mmJSON format	3hg0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3hg0_validation.pdf.gz	456.8 KB	Display	wwPDB validaton report
Full document	3hg0_full_validation.pdf.gz	473.5 KB	Display
Data in XML	3hg0_validation.xml.gz	27.9 KB	Display
Data in CIF	3hg0_validation.cif.gz	39.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hg/3hg0 ftp://data.pdbj.org/pub/pdb/validation_reports/hg/3hg0	HTTPS FTP

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Related structure data

Related structure data	2focS 2jabS 1svx 2bkk 2j8s 2p2c 2v5q S: Starting model for refinement
Similar structure data	2gz3-3 2gz3-2 3q11-d 3pyx-d 3wa5-d 4n80-d 4r3w-d 2gyy-2 2gz1-d 1m7x-2 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 (1)

Deposited unit

A: Baseplate protein

B: Baseplate protein

C: Baseplate protein

D: Designed Ankyrin Repeat Protein (DARPin) 20

68.7 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	46.650, 80.440, 182.870
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Baseplate protein / BPP Mass: 17994.123 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus phage TP901-1 (virus) / Gene: bpp, bppL / Plasmid: pDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): T7 express Iq pLysS / References: UniProt: Q9G096
#2: Protein	Designed Ankyrin Repeat Protein (DARPin) 20 Mass: 14737.599 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) artificial gene (others) / Plasmid: pDST067 / Production host: Escherichia coli (E. coli)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 446 / 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: 2.5 Å³/Da / Density % sol: 50.73 %
Crystal grow	Temperature: 293 K / pH: 6 Details: 40 mM Tris, 20 mM Bis-Tris-Propane, 25% PEG 2000 MME, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.976
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 18, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.976 Å / Relative weight: 1
Reflection	Resolution: 2.1→19.89 Å / Num. obs: 39881 / % possible obs: 97 % / Observed criterion σ(I): 2.48 / Redundancy: 3.58 % / B_iso Wilson estimate: 33.23 Å² / R_merge(I) obs: 0.065 / Net I/σ(I): 12.43
Reflection shell	Resolution: 2.1→2.3 Å / Redundancy: 3.67 % / R_merge(I) obs: 0.5021 / Mean I/σ(I) obs: 2.48 / % possible all: 91.8

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Processing

Software

Name	Version	Classification
MxCuBE		data collection
AMoRE		phasing
PHENIX	(phenix.refine: 1.4_56)	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2JAB AND 2FOC

2jab

2foc

Resolution: 2.1→19.89 Å / SU ML: 0.3 / Isotropic thermal model: Isotropic / σ(F): 1.99 / Stereochemistry target values: ENGH & HUBER

	R_factor	Num. reflection	% reflection
R_free	0.243	997	2.5 %
R_work	0.208	-	-
obs	0.209	39860	97 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 45.08 Å² / k_sol: 0.3 e/Å³

Displacement parameters

B_iso mean: 50.02 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-8.138 Å²	0 Å²	-0 Å²
2-	-	9.688 Å²	0 Å²
3-	-	-	-1.549 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→19.89 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3881	0	0	446	4327

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.014	4020
X-RAY DIFFRACTION	f_angle_d	1.676	5469
X-RAY DIFFRACTION	f_dihedral_angle_d	18.836	1437
X-RAY DIFFRACTION	f_chiral_restr	0.136	623
X-RAY DIFFRACTION	f_plane_restr	0.007	714

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.1-2.2106	0.3383	141	0.3288	5510	X-RAY DIFFRACTION	98
2.2106-2.3489	0.4866	126	0.438	4899	X-RAY DIFFRACTION	87
2.3489-2.5299	0.2956	145	0.2827	5647	X-RAY DIFFRACTION	100
2.5299-2.7839	0.2979	145	0.2392	5660	X-RAY DIFFRACTION	100
2.7839-3.1853	0.2402	145	0.2093	5670	X-RAY DIFFRACTION	100
3.1853-4.0078	0.2184	146	0.1741	5670	X-RAY DIFFRACTION	98
4.0078-19.8904	0.1671	149	0.142	5807	X-RAY DIFFRACTION	97

Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

ID	Method	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	refined	5.8631	-1.6111	-1.2024	0.973	0.3074	0.2491	0.1188	0.5543	-0.0146	0.286	0.0326	0.0329	-0.037	-0.1	-0.2004	0.5285	0.2476	0.0325	0.8024	-0.0355	0.3911	49.6152	3.4781	51.5753
2		2.2769	0.28	-1.5938	0.8529	0.2555	1.3595	-0.154	-0.5349	0.3858	-0.0757	0.2416	0.0632	0.064	0.03	-0.0285	0.3441	-0.0304	-0.0162	0.4977	0.0657	0.2754
3		0.5523	-0.0044	0.1833	0.2195	-0.1625	0.4495	-0.0297	-0.1479	-0.0645	0.0356	0.1092	-0.0172	-0.0979	0.203	-0.0769	0.1139	-0.0341	-0.0026	0.3477	-0.0207	0.1023
4		0.6005	-0.0772	-0.1739	0.0287	0.0109	0.0839	-0.0005	-0.2203	-0.0111	0.1009	0.0296	0.0518	-0.0322	0.1091	-0.0042	0.1899	-0.0873	0.0303	0.249	-0.0261	0.2028
5		0.1658	-0.0087	-0.0984	0.1067	0.3445	0.3897	0.0297	0.0021	0.0593	0.0226	0.0582	-0.0457	0.0094	0.1189	-0.0664	0.1114	-0.0689	0.0179	0.4573	-0.025	0.117
6		5.8161	0.8101	6.3577	1.662	2.6513	8.9895	-0.0814	-0.7697	-0.2781	-0.4191	0.4182	0.16	-1.5994	-1.2546	-0.0838	0.6964	0.2184	0.0433	0.6057	0.1333	0.3973
7		0.2568	0.1944	0.2425	0.6543	0.4539	0.3678	-0.0859	-0.021	0.1498	-0.0282	0.0503	0.0604	-0.1621	-0.143	0.0506	0.2762	-0.0849	-0.0013	0.5359	-0.0044	0.1953
8		1.6408	0.3899	-1.5424	1.0281	0.3027	2.5392	-0.0261	-0.1255	0.0699	-0.0038	0.1386	-0.1274	-0.5013	0.6367	-0.0418	0.157	-0.2045	0.0581	0.5095	-0.0453	0.138
9		3.7337	-1.0412	-0.8509	2.3077	0.0752	0.2326	-0.2542	-0.7377	0.0638	0.3135	0.2742	-0.1543	-0.213	0.7036	-0.1502	0.3747	-0.3212	0.0259	0.7643	-0.1574	0.2651
10		0.3692	0.8135	0.827	1.8755	1.6495	1.8579	-0.0566	0.0629	-0.0595	-0.0886	0.3562	-0.3445	-0.1312	0.841	-0.2894	0.1374	-0.1116	0.0155	0.6044	-0.0542	0.2131
11		0.2395	0.4438	0.5134	1.2008	0.5497	1.4418	-0.1143	-0.134	-0.0548	-0.0205	0.1323	-0.2512	-0.0073	0.4561	-0.0561	0.1595	-0.1619	0.0212	0.631	-0.0724	0.2329
12		0.3285	0.1051	-0.1068	0.4065	1.0791	3.3511	-0.4826	-0.0245	-0.0712	-0.3083	0.1854	-0.4218	-0.315	-0.1169	0.12	0.9138	0.0421	0.0907	0.6471	-0.1238	0.801
13		0.1206	0.2783	0.4071	0.8612	1.1076	1.5106	0.1986	-0.0236	0.1136	-0.1796	-0.2035	-0.0168	-0.2937	-0.6231	-0.0043	0.435	-0.0037	0.0891	0.4617	0.0407	0.2566
14		1.3382	-1.049	-0.2024	0.9641	-0.116	0.3108	0.1026	0.1869	0.1341	0.0988	-0.048	-0.1247	0.044	0.3641	-0.0102	0.2006	-0.0373	-0.0449	0.6247	-0.057	0.1771
15		0.3415	-0.0406	0.4292	0.1874	0.0475	0.7725	0.0985	-0.0753	-0.001	0.0905	-0.0306	-0.0089	-0.0633	0.1082	-0.0362	0.197	-0.0112	-0.0282	0.683	-0.0564	0.1746
16		0.2382	-0.1313	0.1739	0.0904	0.0022	0.8886	-0.0193	0.0554	0.0218	0.2065	-0.0687	0.0056	0.4314	-0.2369	0.1091	0.2164	-0.0328	-0.0521	0.5716	-0.0436	0.1227
17		0.6629	-0.1848	0.5782	0.5312	-0.0941	0.7766	-0.0311	-0.4079	0.0703	0.0669	0.1045	-0.1605	-0.0409	0.6074	-0.0841	0.1306	-0.0097	-0.0332	0.5758	-0.058	0.1424
18		0.8767	0.6255	1.9116	0.4587	1.4013	4.1492	-0.3288	-0.2944	0.2182	0.1344	-0.1381	0.1676	0.6142	-0.4135	0.2826	0.1979	-0.0491	0.0531	0.4117	-0.0615	0.0841
19		0.0331	0.1598	0.0048	0.7383	0.0117	0.0201	-0.0366	-0.9849	0.1533	0.091	-0.4196	0.0482	0.2197	-0.0843	0.2652	0.3116	0.2786	0.1359	-0.9545	-0.0971	0.2098
20		1.6118	-0.2298	1.5111	0.4996	-1.143	5.2705	0.0202	-0.1168	-0.0057	-0.0651	-0.1786	0.0298	0.4215	0.6445	0.1304	0.1164	-0.0018	0.0037	0.3087	-0.0494	0.0813
21		0.0867	0.2819	-0.1287	1.078	-0.3892	1.2964	0.0852	0.0737	0.0905	-0.0523	-0.1184	-0.4538	-0.0036	0.5388	-0.0244	0.1864	0.0741	0.0334	0.5952	-0.0242	0.1848
22		1.2686	-0.717	-0.9341	0.4712	0.4065	0.9473	-0.0832	-0.0406	0.2777	-0.0729	-0.0083	-0.3318	-0.1074	0.6571	-0.0264	0.1654	0.0272	0.0566	0.4977	-0.029	0.2081
23		0.0988	0.2048	0.2168	0.8155	0.7381	1.0655	-0.1233	-0.1151	0.0796	-0.026	0.392	-0.5064	-0.0363	1.0696	-0.2123	0.1589	0.01	0.103	0.7686	-0.0215	0.3685
24		0.0245	0.0963	0.1566	5.0037	2.2255	1.5152	0.6127	0.0273	0.9094	0.0687	-0.1575	-1.7262	0.1107	0.2364	-0.3838	0.2296	0.1638	0.0049	1.2111	-0.1132	0.5705

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	(chain A and resid 33:38)	A	33 - 38
2	X-RAY DIFFRACTION	2	(chain A and resid 39:56)	A	39 - 56
3	X-RAY DIFFRACTION	3	(chain A and resid 57:106)	A	57 - 106
4	X-RAY DIFFRACTION	4	(chain A and resid 107:118)	A	107 - 118
5	X-RAY DIFFRACTION	5	(chain A and resid 119:169)	A	119 - 169
6	X-RAY DIFFRACTION	6	(chain B and resid 34:45)	B	34 - 45
7	X-RAY DIFFRACTION	7	(chain B and resid 46:72)	B	46 - 72
8	X-RAY DIFFRACTION	8	(chain B and resid 73:97)	B	73 - 97
9	X-RAY DIFFRACTION	9	(chain B and resid 98:118)	B	98 - 118
10	X-RAY DIFFRACTION	10	(chain B and resid 119:137)	B	119 - 137
11	X-RAY DIFFRACTION	11	(chain B and resid 138:163)	B	138 - 163
12	X-RAY DIFFRACTION	12	(chain C and resid 32:38)	C	32 - 38
13	X-RAY DIFFRACTION	13	(chain C and resid 39:60)	C	39 - 60
14	X-RAY DIFFRACTION	14	(chain C and resid 61:80)	C	61 - 80
15	X-RAY DIFFRACTION	15	(chain C and resid 81:106)	C	81 - 106
16	X-RAY DIFFRACTION	16	(chain C and resid 107:118)	C	107 - 118
17	X-RAY DIFFRACTION	17	(chain C and resid 119:163)	C	119 - 163
18	X-RAY DIFFRACTION	18	(chain D and resid 12:25)	D	12 - 25
19	X-RAY DIFFRACTION	19	(chain D and resid 26:42)	D	26 - 42
20	X-RAY DIFFRACTION	20	(chain D and resid 43:58)	D	43 - 58
21	X-RAY DIFFRACTION	21	(chain D and resid 59:80)	D	59 - 80
22	X-RAY DIFFRACTION	22	(chain D and resid 81:90)	D	81 - 90
23	X-RAY DIFFRACTION	23	(chain D and resid 91:121)	D	91 - 121
24	X-RAY DIFFRACTION	24	(chain D and resid 122:135)	D	122 - 135

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