PDB-5fwo: Llama nanobody PorM_130

ID or keywords:

Entry

Database: PDB / ID: 5fwo

Title

Llama nanobody PorM_130

Components

NANOBODY

Keywords

IMMUNE SYSTEM / TYPE-9 SECRETION SYSTEM (T9SS) / NANOBODY

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta

Function and homology information

Biological species

LAMA GLAMA (llama)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Leone, P. / Roussel, A.

Citation

Journal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Camelid nanobodies used as crystallization chaperones for different constructs of PorM, a component of the type IX secretion system from Porphyromonas gingivalis.
Authors: Duhoo, Y. / Roche, J. / Trinh, T.T.N. / Desmyter, A. / Gaubert, A. / Kellenberger, C. / Cambillau, C. / Roussel, A. / Leone, P.

History

Deposition	Feb 18, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 3, 2017	Provider: repository / Type: Initial release
Revision 1.1	May 10, 2017	Group: Database references
Revision 1.2	May 17, 2017	Group: Database references
Revision 1.3	Jan 10, 2024	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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4	Oct 9, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5fwo.cif.gz	67.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5fwo.ent.gz	51.4 KB	Display	PDB format
PDBx/mmJSON format	5fwo.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5fwo_validation.pdf.gz	419.3 KB	Display	wwPDB validaton report
Full document	5fwo_full_validation.pdf.gz	419.4 KB	Display
Data in XML	5fwo_validation.xml.gz	8 KB	Display
Data in CIF	5fwo_validation.cif.gz	10.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fw/5fwo ftp://data.pdbj.org/pub/pdb/validation_reports/fw/5fwo	HTTPS FTP

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Related structure data

Related structure data	5lmjC 5lmwC 5lz0C 4fhbS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5nlu-d 6fys-6 5lz0-1 5nml-9 5nm0-4 3kyz-d 3mfg-3 3d1p-d 3b9v-1 4e3b-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#136 - Apr 2011 Nanobodies similarity (1) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: NANOBODY

15 kDa, 1 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)	54.539, 54.539, 126.725
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	178
Space group name H-M	P6₁22

Components on special symmetry positions

ID	Model	Components
1	1	A-2017- HOH

#1: Antibody	NANOBODY Mass: 14994.608 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) LAMA GLAMA (llama) / Plasmid: PHEN6 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): ROSETTA PLYSS
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.96 Å³/Da / Density % sol: 37.2 % / Description: NONE
Crystal grow	pH: 7 / Details: 0.2M AMMONIUM CITRATE DIBASIC 20% PEG3350, pH 7.0

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801
Detector	Type: ADSC CCD / Detector: CCD / Date: Oct 10, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9801 Å / Relative weight: 1
Reflection	Resolution: 1.7→50 Å / Num. obs: 13038 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 21 % / B_iso Wilson estimate: 26.78 Å² / R_merge(I) obs: 0.08 / Net I/σ(I): 24.6
Reflection shell	Resolution: 1.7→1.79 Å / Redundancy: 21.1 % / R_merge(I) obs: 1.36 / Mean I/σ(I) obs: 2.4 / % possible all: 99.6

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Processing

Software

Name	Version	Classification
BUSTER	2.10.2	refinement
XDS		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4FHB

4fhb

Resolution: 1.7→44.26 Å / Cor.coef. F_o:F_c: 0.9578 / Cor.coef. F_o:F_c free: 0.927 / SU R Cruickshank DPI: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.128 / SU R_free Blow DPI: 0.118 / SU R_free Cruickshank DPI: 0.11
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2223	679	5.24 %	RANDOM
R_work	0.1861	-	-	-
obs	0.188	12963	99.95 %	-

Displacement parameters

B_iso mean: 34.68 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.1419 Å²	0 Å²	0 Å²
2-	-	-1.1419 Å²	0 Å²
3-	-	-	2.2838 Å²

Refine analyze

Luzzati coordinate error obs: 0.229 Å

Refinement step

Cycle: LAST / Resolution: 1.7→44.26 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	981	0	0	108	1089

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.01	1027	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	1.05	1394	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		355	SINUSOIDAL	2
X-RAY DIFFRACTION	t_incorr_chiral_ct
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_trig_c_planes		19	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes		163	HARMONIC	5
X-RAY DIFFRACTION	t_it		1027	HARMONIC	20
X-RAY DIFFRACTION	t_nbd
X-RAY DIFFRACTION	t_omega_torsion	3.74
X-RAY DIFFRACTION	t_other_torsion	14.73
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_chiral_improper_torsion		130	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact		1356	SEMIHARMONIC	4

LS refinement shell

Resolution: 1.7→1.84 Å / Total num. of bins used: 7

	R_factor	Num. reflection	% reflection
R_free	0.2489	133	5.15 %
R_work	0.2375	2451	-
all	0.2381	2584	-
obs	-	-	99.88 %

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	0.035	0.4786	8.1326	0.9842	-2.0277	3.2299	-0.1913	-0.1817	0.2664	0.3252	0.0952	0.501	0.0763	0.3924	0.0961	-0.028	0.2118	0.003	0.0828	-0.1181	-0.0902	-8.4147	-13.9443	12.1508
2	7.9607	-1.9284	-1.4335	0.4338	-0.6224	4.0859	-0.3919	0.4638	0.3849	0.004	0.2789	-0.492	0.3398	0.9564	0.113	-0.155	0.0047	-0.0374	0.1379	-0.0715	-0.0311	5.0349	-16.4229	-2.5838
3	7.5683	0.4783	-2.1109	4.1951	1.2056	1.0333	-0.2254	0.3658	0.139	0.0136	0.3076	-0.2528	0.0701	0.6259	-0.0822	-0.1156	0.0181	-0.0118	0.0344	0.0002	-0.0853	1.5749	-20.4936	-5.5939
4	2.0343	1.2866	-0.4727	0.8078	2.876	4.4834	0.0237	-0.4213	0.125	0.6877	-0.4331	0.1849	0.5307	0.118	0.4094	0.2095	0.0577	0.085	-0.0056	-0.0614	-0.077	-12.5444	-19.3681	10.8929
5	0.9808	-0.224	-0.1875	10.2617	-2.4377	7.2885	0.0066	-0.7432	0.2007	0.6724	-0.3714	0.3448	0.3214	-0.2003	0.3648	-0.0491	-0.1	0.0512	-0.0396	-0.1046	-0.1401	-17.0006	-19.4006	4.3418
6	2.5749	-2.5753	0.31	1.1966	-2.1487	6.757	-0.179	-0.0234	0.6097	0.0786	0.0742	0.0634	-0.7959	0.6264	0.1048	-0.0062	-0.0874	-0.0683	-0.1082	0.0035	-0.0055	-5.3828	-8.3679	-4.1059
7	-0.2859	-0.5034	-2.3206	10.1071	-1.5146	2.4893	-0.151	0.0749	0.5461	0.0731	0.0014	0.0947	-0.9075	0.2898	0.1496	0.2372	-0.1445	-0.1565	-0.1462	0.0645	0.0252	-6.6373	-2.0583	-5.9034
8	1.668	0.406	0.8797	3.4499	1.8304	6.4276	-0.1631	-0.1306	0.2257	0.2025	-0.3236	0.3143	0.0295	-0.3591	0.4867	-0.045	-0.0194	-0.0195	-0.0637	-0.0601	0.0249	-15.6913	-16.8304	-4.117
9	1.4594	-1.4561	0.923	0.8062	2.2556	6.7645	-0.2195	0.1378	0.2918	0.005	-0.1477	0.2731	-0.0425	-0.1572	0.3672	-0.0721	-0.0162	-0.0494	-0.1138	0.0009	-0.0343	-14.1641	-18.0157	-9.9486
10	5.0581	0.4718	2.8895	3.275	2.3719	4.1102	-0.3993	0.3733	0.0921	-0.2743	0.0823	-0.0281	0.0549	0.405	0.317	-0.029	-0.0158	-0.032	-0.0664	0.0073	-0.1026	-7.2124	-19.4979	-11.0197
11	1.1126	2.5305	4.8013	2.8991	-2.0961	0	-0.0329	-0.7796	-0.4218	0.9939	-0.31	-0.0719	1.0752	-0.056	0.3429	0.4015	0.014	0.076	0.0868	0.1074	-0.0036	-12.3558	-27.2021	4.0544
12	3.2958	0.1456	-0.0005	7.4497	4.145	2.3295	-0.1158	-0.3718	0.1492	0.6956	0.1496	0.1955	0.6044	-0.449	-0.0338	-0.0384	0.0579	0.0011	-0.0026	0.0447	-0.1594	-8.0206	-22.8819	1.8833
13	6.3633	2.2205	-4.5644	5.9322	-2.6184	4.8948	-0.004	0.2623	0.1727	-0.2711	0.1927	-0.2808	-0.3893	0.701	-0.1886	-0.0215	-0.0439	0.0004	0.059	0.0025	-0.0699	0.1876	-18.5619	-11.419
14	1.4569	-2.0486	-0.686	7.6165	1.1644	0.6001	0.1012	0.3181	0.4026	-0.6017	0.0406	-0.4127	-0.37	0.5654	-0.1417	0.0863	-0.1709	-0.0369	0.1821	0.0499	0.0781	1.1602	-9.2731	-9.0402
15	3.8186	0.7168	-0.6582	1.5925	2.1474	6.6855	-0.2312	-0.4129	0.2755	0.041	-0.2753	0.3353	0.005	-0.3831	0.5064	-0.0304	0.0079	-0.0307	-0.0578	-0.0778	0.0633	-13.5956	-13.1731	1.4318
16	-3.3046	4.5348	0.9509	6.3379	-3.0079	0.0042	0.1896	-0.3397	0.2711	0.0703	-0.4498	0.6458	-0.2753	-1.0177	0.2602	-0.137	0.0355	-0.0631	0.16	-0.1871	0.276	-24.7869	-16.0106	-2.3836
17	1.9678	2.1921	-2.3773	1.8753	-7.8559	5.6722	0.1041	0.0355	-0.1478	-0.1611	-0.0494	0.2936	-0.4289	-0.0501	-0.0547	0.0098	0.125	-0.1381	0.0001	-0.0998	0.1651	-20.3313	-10.6126	-8.7896
18	-1.95	1.0904	-2.0325	7.0659	-1.6532	1.2627	-0.0067	0.1387	0.6076	0.1138	-0.1628	0.0668	-0.4046	-0.2734	0.1695	0.0113	0.0746	-0.0962	-0.0186	-0.1418	0.1677	-18.5106	-7.3467	-0.087
19	-0.465	-1.7423	-3.9871	8.4567	5.1861	18.2468	-0.1515	-0.535	0.3123	0.5411	0.0368	0.1779	0.1361	-0.0304	0.1147	-0.0805	0.0145	-0.0524	-0.1463	-0.0732	-0.0976	-10.7493	-10.2832	6.5397
20	6.1637	-2.8853	-1.2759	2.5462	-0.4896	0.2272	-0.3771	0.4466	0.2453	-0.2023	0.3712	-0.7142	-0.1991	0.6451	0.0059	-0.0172	-0.1643	-0.0083	0.1973	0.0021	0.0817	4.9353	-11.5094	-4.7676

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	{ A\|2 - 6 }
2	X-RAY DIFFRACTION	2	{ A\|7 - 14 }
3	X-RAY DIFFRACTION	3	{ A\|15 - 22 }
4	X-RAY DIFFRACTION	4	{ A\|23 - 29 }
5	X-RAY DIFFRACTION	5	{ A\|30 - 36 }
6	X-RAY DIFFRACTION	6	{ A\|37 - 42 }
7	X-RAY DIFFRACTION	7	{ A\|43 - 47 }
8	X-RAY DIFFRACTION	8	{ A\|48 - 54 }
9	X-RAY DIFFRACTION	9	{ A\|55 - 65 }
10	X-RAY DIFFRACTION	10	{ A\|66 - 72 }
11	X-RAY DIFFRACTION	11	{ A\|73 - 77 }
12	X-RAY DIFFRACTION	12	{ A\|78 - 82 }
13	X-RAY DIFFRACTION	13	{ A\|83 - 88 }
14	X-RAY DIFFRACTION	14	{ A\|89 - 94 }
15	X-RAY DIFFRACTION	15	{ A\|95 - 103 }
16	X-RAY DIFFRACTION	16	{ A\|104 - 108 }
17	X-RAY DIFFRACTION	17	{ A\|109 - 113 }
18	X-RAY DIFFRACTION	18	{ A\|114 - 118 }
19	X-RAY DIFFRACTION	19	{ A\|119 - 124 }
20	X-RAY DIFFRACTION	20	{ A\|125 - 130 }

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