PDB-4i0c: The structure of the camelid antibody cAbHuL5 in complex with hum...

ID or keywords:

Entry

Database: PDB / ID: 4i0c

Title

The structure of the camelid antibody cAbHuL5 in complex with human lysozyme

Components

Lysozyme C
cAbHuL5 antibody

Keywords

IMMUNE SYSTEM/HYDROLASE /

beta-barrel /

alpha-beta protein /

immune recognition / glycosidase /

IMMUNE SYSTEM-HYDROLASE complex

Function / homology

Function and homology information

antimicrobial humoral response /

Antimicrobial peptides /

metabolic process / specific granule lumen / azurophil granule lumen / tertiary granule lumen /

lysozyme /

lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium ...
Similarity search - Function

Biological species

Homo sapiens (human)

Camelus dromedarius (Arabian camel)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

De Genst, E. / Chan, P.H. / Pardon, E. / Kumita, J.R. / Christodoulou, J. / Menzer, L. / Chirgadze, D.Y. / Robinson, C.V. / Muyldermans, S. / Matagne, A. ...

Citation

Journal: J.Phys.Chem.B / Year: 2013
Title: A nanobody binding to non-amyloidogenic regions of the protein human lysozyme enhances partial unfolding but inhibits amyloid fibril formation.
Authors: De Genst, E. / Chan, P.H. / Pardon, E. / Hsu, S.T. / Kumita, J.R. / Christodoulou, J. / Menzer, L. / Chirgadze, D.Y. / Robinson, C.V. / Muyldermans, S. / Matagne, A. / Wyns, L. / Dobson, C.M. / Dumoulin, M.

History

Deposition	Nov 16, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 9, 2013	Provider: repository / Type: Initial release
Revision 1.1	Nov 6, 2013	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4i0c.cif.gz	215.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4i0c.ent.gz	183.9 KB	Display	PDB format
PDBx/mmJSON format	4i0c.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i0/4i0c ftp://data.pdbj.org/pub/pdb/validation_reports/i0/4i0c	HTTPS FTP

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Related structure data

Similar structure data	3sxu-d 3lif-2 2i7s-2 3swv-d 1pbv-d 4n1d-1 3by9-2 2qcq-d 5crc-2 3by9-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #162 - Jun 2013 Dermcidin similarity (1) #193 - Jan 2016 Siderocalin similarity (1)

Deposited unit

A: Lysozyme C

B: Lysozyme C

C: cAbHuL5 antibody

D: cAbHuL5 antibody

hetero molecules

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

1

A: Lysozyme C

D: cAbHuL5 antibody

hetero molecules

defined by author&software
29.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Lysozyme C

C: cAbHuL5 antibody

hetero molecules

defined by author&software
29.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	96.321, 96.321, 156.750
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-202- CL
2	1	B-203- CL
3	1	A-393- HOH
4	1	B-328- HOH
5	1	B-353- HOH

#1: Protein	Lysozyme C / 1 / 4-beta-N-acetylmuramidase C Mass: 14720.693 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LYZ, LZM / Production host: Komagataella pastoris (fungus) / References: UniProt: P61626, lysozyme
#2: Antibody	cAbHuL5 antibody Mass: 14602.104 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Escherichia coli (E. coli)
#3: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 373 / 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: 3.1 Å³/Da / Density % sol: 60.32 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 4.8 M NaCl, 0.1 M HEPES pH 7, 3% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: BW7A / Wavelength: 0.8125 Å
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 13, 2005
Radiation	Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8125 Å / Relative weight: 1
Reflection	Resolution: 1.95→19.913 Å / Num. all: 54358 / Num. obs: 54358 / % possible obs: 99.94 % / Observed criterion σ(F): 1.35 / Observed criterion σ(I): 1.35
Reflection shell	Resolution: 1.95→2.02 Å / % possible all: 99.9

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.7.3_928)	refinement
DENZO		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.95→19.913 Å / SU ML: 0.25 / σ(F): 1.35 / Phase error: 20.09 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2186	2762	5.08 %	random
R_work	0.1871	-	-	-
all	0.1887	54358	-	-
obs	0.1887	54358	99.94 %	-

Solvent computation

Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 36.451 Å² / k_sol: 0.406 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.3674 Å²	-0 Å²	0 Å²
2-	-	-1.3674 Å²	-0 Å²
3-	-	-	2.7349 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→19.913 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3936	0	19	373	4328

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4105
X-RAY DIFFRACTION	f_angle_d	1.014	5548
X-RAY DIFFRACTION	f_dihedral_angle_d	13.183	1460
X-RAY DIFFRACTION	f_chiral_restr	0.073	570
X-RAY DIFFRACTION	f_plane_restr	0.004	723

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 (%)
1.95-1.9836	0.342	134	0.2877	2536	X-RAY DIFFRACTION	100
1.9836-2.0197	0.2812	137	0.2302	2535	X-RAY DIFFRACTION	100
2.0197-2.0585	0.2572	134	0.2092	2546	X-RAY DIFFRACTION	100
2.0585-2.1004	0.2448	145	0.195	2538	X-RAY DIFFRACTION	100
2.1004-2.1461	0.221	147	0.1818	2537	X-RAY DIFFRACTION	100
2.1461-2.1959	0.2346	148	0.1875	2530	X-RAY DIFFRACTION	100
2.1959-2.2508	0.2321	131	0.1844	2536	X-RAY DIFFRACTION	100
2.2508-2.3115	0.2154	148	0.181	2540	X-RAY DIFFRACTION	100
2.3115-2.3795	0.2212	145	0.1917	2549	X-RAY DIFFRACTION	100
2.3795-2.4561	0.2344	124	0.1884	2572	X-RAY DIFFRACTION	100
2.4561-2.5437	0.242	128	0.1889	2562	X-RAY DIFFRACTION	100
2.5437-2.6454	0.2298	137	0.1962	2560	X-RAY DIFFRACTION	100
2.6454-2.7655	0.2199	123	0.1998	2595	X-RAY DIFFRACTION	100
2.7655-2.9108	0.2628	126	0.2091	2594	X-RAY DIFFRACTION	100
2.9108-3.0926	0.2197	129	0.2109	2591	X-RAY DIFFRACTION	100
3.0926-3.3304	0.2358	143	0.1901	2596	X-RAY DIFFRACTION	100
3.3304-3.6636	0.1873	141	0.1689	2601	X-RAY DIFFRACTION	100
3.6636-4.1895	0.1844	133	0.1451	2643	X-RAY DIFFRACTION	100
4.1895-5.2621	0.1642	157	0.1439	2655	X-RAY DIFFRACTION	100
5.2621-19.9136	0.2221	152	0.2232	2780	X-RAY DIFFRACTION	99

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	4.5815	1.0543	-1.3569	4.5903	-3.5452	8.2059	0.1202	-0.1032	0.5503	0.2536	0.1151	0.4127	-0.6287	-0.2688	-0.1899	0.1769	0.024	0.024	0.1158	-0.0229	0.185	20.3101	61.5177	125.6481
2	0.8057	1.0447	-1.4008	3.0979	-3.1118	5.2501	0.0884	-0.0027	-0.0158	0.0346	-0.0727	0.2014	-0.0133	0.0687	-0.0131	0.1032	-0.0012	-0.004	0.1315	-0.0118	0.1425	23.6685	53.4534	118.6221
3	6.8332	-7.3236	-0.1087	8.7907	-0.8551	1.0026	-0.4025	-0.4589	-0.5987	0.3261	0.3075	0.1682	0.1364	0.027	0.067	0.1597	-0.0125	0.0333	0.1735	0.0888	0.2791	31.4404	45.4602	133.5091
4	2.149	-0.2097	0.9826	1.5066	-1.086	3.5892	0.0859	-0.0817	-0.0738	-0.0189	-0.1029	-0.1345	0.0969	0.14	-0.0002	0.0966	-0.0055	0.0105	0.1059	0.0196	0.1183	37.1258	50.9801	126.1905
5	4.3383	1.0674	-3.82	0.7764	-1.0172	7.3723	-0.3547	0.087	-0.6482	-0.4391	0.1589	-0.6153	0.4576	0.1832	0.7269	0.1965	-0.019	0.221	0.1942	-0.0612	0.4084	30.718	44.8423	115.7417
6	9.5118	-5.0917	4.8762	6.763	-4.4835	3.5725	-0.1294	0.158	0.0602	-0.2598	-0.068	-0.0654	0.0984	-0.0834	0.1698	0.2238	-0.0338	0.0667	0.14	-0.0172	0.1812	19.059	42.7464	118.6066
7	4.1924	2.5933	-1.2913	1.7683	-0.0709	3.6523	-0.0714	-0.1483	0.2536	0.0295	0.0819	0.585	-0.4744	-0.5636	-0.0383	0.1683	0.1098	0.0146	0.3887	0.0385	0.2769	12.6864	56.8573	119.0871
8	5.7987	0.6583	0.5961	1.9144	-2.3309	6.0886	-0.2112	-0.2692	0.3973	0.2395	0.2866	0.0357	-0.5068	-0.1417	-0.1341	0.188	0.0465	-0.0086	0.1106	-0.0165	0.1758	21.0938	61.7804	47.999
9	1.0586	0.1079	-0.7519	0.7802	0.3954	0.8224	-0.0952	-0.072	-0.2642	0.1017	-0.0667	-0.0596	0.089	0.0217	0.0984	0.0722	0.0031	-0.0022	0.1017	0.0327	0.1391	27.1597	50.503	46.5983
10	3.1117	-0.7647	1.3257	1.3846	-0.5373	3.6931	0.0463	-0.053	-0.0922	-0.0089	-0.0404	-0.0697	0.0427	0.0999	0.0019	0.067	-0.0097	0.0024	0.0786	0.0287	0.1021	37.7893	51.1298	48.1594
11	8.9828	3.8061	-6.67	3.3806	-3.6005	5.2894	-0.7341	0.1386	-0.7069	-0.6804	0.4326	-0.7124	0.847	0.2384	0.3447	0.2336	0.013	0.0619	0.1753	-0.0248	0.2723	30.8446	44.2928	38.2641
12	5.6822	-4.3402	5.2115	7.7297	-5.253	9.4744	0.0516	0.1906	-0.1588	-0.2085	-0.1349	0.1533	0.3446	-0.1776	0.1314	0.1774	-0.037	0.0662	0.1276	-0.0299	0.1508	19.2203	42.7957	41.5771
13	2.452	2.1519	0.5286	2.1868	0.22	0.9421	0.0074	-0.0672	0.0106	0.1273	-0.0118	0.4419	-0.1586	-0.1533	0.005	0.1483	0.0342	0.0324	0.2652	0.018	0.233	13.2077	57.003	42.031
14	1.8296	-0.3864	-0.5839	1.451	-0.5117	3.5341	-0.3767	0.8382	-0.0564	-0.0429	0.2238	0.0304	0.0972	-0.0281	0.1543	0.1634	0.0071	-0.0381	0.1072	0.0279	0.1273	8.1559	54.7685	13.0479
15	2.4691	3.0653	1.1105	6.8385	-0.8783	3.7436	0.1707	0.2592	-0.8281	-0.2367	0.1181	-0.5802	0.1554	0.595	-0.2512	0.1526	0.0301	0.0037	0.2592	-0.0282	0.1551	15.7391	51.3268	15.6734
16	2.4438	-1.9306	2.2672	5.2346	0.4969	4.1621	0.2242	0.3388	0.3888	-0.2435	-0.402	-0.283	-0.0307	0.2982	0.0498	0.1268	-0.034	0.015	0.2042	0.0561	0.0979	17.3793	58.8053	21.7406
17	5.8088	-3.8482	3.3165	4.2378	-3.5872	4.3599	-0.4191	0.0769	0.8764	0.332	-0.1059	-0.3625	-0.8008	0.0172	0.5386	0.2436	-0.0069	-0.105	0.1507	-0.0055	0.2464	11.6583	62.8557	23.1913
18	3.5619	0.9505	2.771	2.4715	-1.0817	3.7836	0.0611	0.0503	-0.1463	0.0904	-0.0321	-0.3066	0.2022	0.1303	-0.0122	0.1035	-0.0329	-0.0087	0.0768	-0.0161	0.1222	12.2147	51.665	25.2115
19	5.294	0.1972	1.314	3.1893	-4.2789	6.2115	0.0655	-0.1626	0.2235	1.1645	0.1378	0.2692	-0.6753	-0.0771	-0.2111	0.2068	0.0099	0.0313	0.1404	-0.0067	0.122	-1.5286	58.6364	19.2236
20	6.328	-1.1639	3.2628	1.4394	-0.4456	4.197	-0.2494	0.0435	0.3708	-0.0578	0.0202	0.0028	-0.1093	0.1574	0.2223	0.1063	-0.0562	-0.0311	0.0889	0.0803	0.1751	17.4538	63.3996	26.3053
21	6.857	0.6455	3.9694	2.3513	0.7604	5.3108	0.1667	0.1828	-0.2349	0.1428	-0.0936	-0.3045	-0.0211	0.1833	-0.0587	0.1229	-0.0307	-0.0127	0.0704	0.0817	0.1391	11.6105	62.2779	16.6412
22	2.0185	2.5132	0.244	3.3259	-0.315	2.1967	-0.0728	-0.0689	-0.1358	-0.1853	0.0003	-0.3497	0.1651	0.4748	0.0889	0.1796	0.0165	0.0333	0.2566	0.0124	0.1132	14.3575	54.4366	91.025
23	3.8076	0.1564	3.0547	2.8228	-0.0012	3.5569	-0.0419	0.3386	-0.1083	-0.0004	-0.0254	0.0654	-0.1155	0.2436	0.0213	0.1006	-0.0229	0.0071	0.1816	0.0663	0.1323	17.6914	58.9861	99.3466
24	3.1637	-2.2782	3.2495	2.2131	-2.4971	3.4385	-0.5138	0.0542	0.577	0.0952	-0.0645	-0.2381	-0.9694	-0.2024	0.0809	0.3151	0.1357	-0.2129	0.0668	0.0538	0.1277	10.7374	63.1877	100.7382
25	3.7758	0.3764	2.9177	0.8111	-0.1075	2.9987	-0.0364	0.0585	0.0651	-0.0251	-0.0398	-0.0825	0.0175	0.1127	0.0851	0.1079	-0.0024	0.0241	0.0989	0.0209	0.1304	12.7499	56.5432	101.8147
26	6.7474	0.4953	2.5618	2.5369	0.2976	4.9968	0.0482	0.1177	-0.2871	0.0432	-0.022	-0.1456	-0.0761	0.2759	0.0289	0.1199	-0.0172	-0.0144	0.0405	0.0885	0.0955	11.7022	62.353	93.8819

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 1:14)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 15:36)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 37:50)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 51:101)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 102:109)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 110:121)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 122:130)
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 1:14)
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 15:50)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 51:101)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 102:109)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 110:121)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 122:130)
14	X-RAY DIFFRACTION	14	chain 'C' and (resseq 2:17)
15	X-RAY DIFFRACTION	15	chain 'C' and (resseq 18:26)
16	X-RAY DIFFRACTION	16	chain 'C' and (resseq 27:38)
17	X-RAY DIFFRACTION	17	chain 'C' and (resseq 39:50)
18	X-RAY DIFFRACTION	18	chain 'C' and (resseq 51:81)
19	X-RAY DIFFRACTION	19	chain 'C' and (resseq 82:89)
20	X-RAY DIFFRACTION	20	chain 'C' and (resseq 90:109)
21	X-RAY DIFFRACTION	21	chain 'C' and (resseq 110:127)
22	X-RAY DIFFRACTION	22	chain 'D' and (resseq 1:26)
23	X-RAY DIFFRACTION	23	chain 'D' and (resseq 27:38)
24	X-RAY DIFFRACTION	24	chain 'D' and (resseq 39:50)
25	X-RAY DIFFRACTION	25	chain 'D' and (resseq 51:109)
26	X-RAY DIFFRACTION	26	chain 'D' and (resseq 110:127)

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-Yorodumi

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Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

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Yorodumi