PDB-5lwf: Structure of a single domain camelid antibody fragment cAb-G10S i...

ID or keywords:

Entry

Database: PDB / ID: 5lwf

Title

Structure of a single domain camelid antibody fragment cAb-G10S in complex with the BlaP beta-lactamase from Bacillus licheniformis

Components

Beta-lactamase
Camelid heavy-chain antibody variable fragment cAb-G10S

Keywords

HYDROLASE / vhh / aggregation

Function / homology

Function and homology information

beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / plasma membrane
Similarity search - Function

Biological species

Bacillus licheniformis (bacteria)

Lama glama (llama)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.56 Å

Authors

Vettore, N. / Kerff, F. / Pain, C. / Herman, R. / Sauvage, E. / Preumont, S. / Charlier, P. / Dumoulin, M.

Citation

Journal: To Be Published
Title: Probing the mechanism of aggregation of polyQ model proteins with camelid heavy-chain antibody fragments
Authors: Vettore, N. / Kerff, F. / Pain, C. / Herman, R. / Sauvage, E. / Preumont, S. / Charlier, P. / Dumoulin, M.

History

Deposition	Sep 16, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 15, 2017	Provider: repository / Type: Initial release
Revision 1.1	Oct 16, 2019	Group: Data collection / Category: reflns_shell

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5lwf.cif.gz	309.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5lwf.ent.gz	263.8 KB	Display	PDB format
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Validation report

Summary document	5lwf_validation.pdf.gz	473.9 KB	Display	wwPDB validaton report
Full document	5lwf_full_validation.pdf.gz	485.5 KB	Display
Data in XML	5lwf_validation.xml.gz	26.6 KB	Display
Data in CIF	5lwf_validation.cif.gz	36.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lw/5lwf ftp://data.pdbj.org/pub/pdb/validation_reports/lw/5lwf	HTTPS FTP

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Related structure data

Related structure data	4m3jC 4m3kC 4n1hC C: citing same article (ref.)
Similar structure data	5r9n-d 5tx3-1 2ax4-1 5twy-2 2gae-d 3c5u-d 5a1k-1 6p13-d 3wld-d 2ivz-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	#29 - May 2002 Penicillin-binding Proteins similarity (6) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #164 - Aug 2013 Serotonin Receptor similarity (5) #187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (2) #261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#29 - May 2002
Penicillin-binding Proteins
similarity (6)
#21 - Sep 2001
Antibodies
similarity (1)
#256 - Apr 2021
SARS-CoV-2 Spike and Antibodies
similarity (1)
#164 - Aug 2013
Serotonin Receptor
similarity (5)
#187 - Jul 2015
New Delhi Metallo-β-Lactamase
similarity (2)
#261 - Sep 2021
DNA-Sequencing Nanopores
similarity (1)
#22 - Oct 2001
Photosystem I
similarity (1)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (1)
#95 - Nov 2007
Multidrug Resistance Transporters
similarity (1)

Deposited unit

A: Beta-lactamase

B: Beta-lactamase

C: Camelid heavy-chain antibody variable fragment cAb-G10S

D: Camelid heavy-chain antibody variable fragment cAb-G10S

hetero molecules

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

1

A: Beta-lactamase

C: Camelid heavy-chain antibody variable fragment cAb-G10S

hetero molecules

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

2

B: Beta-lactamase

D: Camelid heavy-chain antibody variable fragment cAb-G10S

hetero molecules

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

Unit cell

Length a, b, c (Å)	47.278, 121.691, 137.029
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Beta-lactamase / Penicillinase Mass: 30412.311 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus licheniformis (bacteria) / Gene: penP, blaP / Production host: Escherichia coli (E. coli) / References: UniProt: P00808, beta-lactamase
#2: Antibody	Camelid heavy-chain antibody variable fragment cAb-G10S Mass: 14587.093 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.19 Å³/Da / Density % sol: 43.83 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M Mg Acetate, 0.1 M NaCacodylate pH 6.5, 20% PEG8000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 26, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97857 Å / Relative weight: 1
Reflection	Resolution: 2.5→45.4593 Å / Num. obs: 54511 / % possible obs: 98.9 % / Redundancy: 3.56 % / B_iso Wilson estimate: 45.36 Å² / Net I/σ(I): 9.72

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Processing

Software

Name	Version	Classification
BUSTER	2.10.2	refinement
XDS		data reduction
XDS		data scaling
PHENIX		phasing

Refinement

Resolution: 2.56→40.5 Å / Cor.coef. F_o:F_c: 0.892 / Cor.coef. F_o:F_c free: 0.87 / R_factor R_free error: 0 / SU R Cruickshank DPI: 1.364 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.289 / SU R_free Blow DPI: 0.303 / SU R_free Cruickshank DPI: 0.309

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.242	1231	4.98 %	RANDOM
R_work	0.215	-	-	-
obs	0.217	24712	93.9 %	-

Displacement parameters

B_iso mean: 56.87 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.5067 Å²	0 Å²	0 Å²
2-	-	4.3568 Å²	0 Å²
3-	-	-	-0.85 Å²

Refine analyze

Luzzati coordinate error obs: 0.44 Å

Refinement step

Cycle: LAST / Resolution: 2.56→40.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5906	0	20	1	5927

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.007	6032	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	1.01	8166	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		2105	SINUSOIDAL	2
X-RAY DIFFRACTION	t_incorr_chiral_ct
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_trig_c_planes		162	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes		873	HARMONIC	5
X-RAY DIFFRACTION	t_it		6032	HARMONIC	20
X-RAY DIFFRACTION	t_nbd
X-RAY DIFFRACTION	t_omega_torsion	2.97
X-RAY DIFFRACTION	t_other_torsion	19.23
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_chiral_improper_torsion		795	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		6694	SEMIHARMONIC	4

LS refinement shell

Resolution: 2.56→2.67 Å / R_factor R_free error: 0 / Total num. of bins used: 12

	R_factor	Num. reflection	% reflection
R_free	0.256	128	4.8 %
R_work	0.221	2539	-
all	0.222	2667	-
obs	-	-	84.51 %

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	2.2363	1.1673	-1.2616	7.474	0.1815	2.2305	0.2352	-0.5702	-0.3728	1.0081	-0.1779	-0.7234	0.2995	0.4472	-0.0573	0.7371	0.19	0.2191	-0.2708	0.0897	-0.0694	14.8828	-31.37	-17.556
2	1.6281	0.5086	3.0086	1.8901	0.2348	5.0403	-0.35	0.1274	-0.2769	0.8575	0.2186	0.4228	-0.042	-0.0934	0.1313	-0.0915	0.1038	0.112	-0.3141	0.0294	-0.0772	7.3412	-21.0592	-28.4457
3	4.7263	-9.1196	-2.0195	0	-1.4201	0.7013	-0.0144	0.3643	-0.1878	0.112	-0.0863	-0.0205	-0.0204	-0.2406	0.1007	-0.5888	-0.0056	-0.111	-0.2841	-0.3092	0.3456	-5.9194	-20.8975	-50.911
4	7.8295	1.3573	-0.674	10.0573	1.4565	4.306	-0.1815	0.5339	-0.3928	0.4335	-0.5074	0.6882	0.2369	-0.6311	0.6888	-0.7561	-0.0062	0.0993	-0.5247	-0.1585	-0.1518	1.8101	-29.3555	-48.6914
5	3.147	1.0519	0.064	3.9392	-0.4656	3.8822	-0.2721	-0.4211	-0.0383	0.1195	0.1861	0.3192	-0.2587	0.0959	0.086	-0.2488	0.0037	-0.0668	-0.3931	-0.0049	-0.0765	11.0916	-15.2259	-38.9266
6	0.2449	-0.4875	-0.4448	1.5244	1.6357	2.4482	-0.0715	0.1505	-0.3238	0.6111	0.1004	-0.0484	0.2119	0.0288	-0.0288	-0.229	0.0782	0.0433	-0.4544	0.0551	-0.1093	12.9651	-21.334	-32.4805
7	2.297	0.4713	0.0988	5.5845	0.5767	1.6008	-0.2552	-0.1455	-0.4481	1.3123	-0.0531	1.3374	0.4147	-0.4856	0.3083	-0.2146	0.0053	0.4316	-0.5054	-0.0312	-0.0436	-0.7711	-27.8407	-29.7254
8	0.9979	1.5778	2.9836	2.353	0.4945	0.2483	-0.0799	-0.0792	-0.1501	0.6976	0.1852	0.2071	0.5485	-0.2829	-0.1054	0.2758	0.1374	0.3091	-0.4846	0.1114	-0.1319	8.8863	-32.595	-22.2598
9	7.9246	0.5722	0.6521	2.7735	1.1957	0.2995	0.1802	0.5898	0.2132	1.8606	0.3021	1.1932	-0.6495	-0.9155	-0.4823	1.1487	0.6753	0.7459	0.3925	0.4381	0.6358	7.6275	-61.8116	-3.8676
10	1.2012	0.8085	-0.3587	9.8993	-4.3859	4.076	-0.2664	-0.046	0.0287	1.7336	0.2582	-0.3185	-1.1043	-0.1607	0.0082	0.2323	0.1451	-0.0612	-0.2782	-0.0435	-0.0715	29.2127	-57.8569	-13.3013
11	4.0372	3.0012	0.1548	4.2098	-0.5561	4.3064	-0.4202	0.8044	0.4175	-0.1642	0.2578	-0.7291	-0.741	-0.0412	0.1624	-0.0646	0.0104	-0.0955	-0.2721	0.1055	0.1098	28.262	-46.2727	-30.7875
12	0	-5.1986	-2.515	6.5254	-1.9567	3.1278	-0.1769	0.0495	0.0054	1.1719	0.2206	-0.235	-0.9021	0.0422	-0.0437	0.0287	0.0294	-0.1432	-0.4068	-0.0335	0.0138	30.5824	-51.0597	-22.2812
13	1.7302	0.3799	-4.2399	7.0284	-1.3927	0.0011	-0.0666	-0.3766	0.0704	0.4143	0.004	-0.2569	-0.0679	0.1434	0.0627	-0.1969	0.0046	-0.0427	-0.355	-0.014	-0.0563	29.8717	-66.752	-18.5014
14	0.0026	0.1814	-1.3239	3.5426	-5.0873	0	-0.1028	0.4859	0.0668	1.4668	0.5164	0.8654	-0.7984	-0.5531	-0.4136	0.0694	0.1709	0.0235	-0.3867	0.0124	-0.1042	21.9954	-64.8227	-14.4284
15	4.0169	1.5034	-0.5577	4.5933	-3.5007	2.5753	0.2591	-0.3349	0.3822	2.9651	0.1334	0.1538	-1.9506	-0.1103	-0.3925	0.8174	0.2323	-0.0179	-0.6595	-0.0003	-0.279	24.768	-51.2148	-7.7769
16	0.0078	0.9709	-2.0832	7.1936	-2.5015	2.6896	0.1199	0.4442	0.3234	1.79	0.9212	1.3345	-0.7884	-0.7354	-1.0411	0.5873	0.5856	0.5011	-0.0101	0.2937	0.2309	13.8348	-57.1752	-9.2812
17	3.1153	-6.3668	-5.5712	0.6631	5.7818	0.0143	0.0885	0.0399	0.4328	0.1223	-0.1334	0.0113	-0.0867	-0.1601	0.045	1.8623	0.7405	0.8883	0.0361	0.4019	0.4867	10.5461	-54.1826	-0.579
18	3.035	-3.0668	-1.4929	10.7383	2.038	0.0013	-0.1366	0.3533	-0.4945	-0.6874	0.2754	0.0869	0.0805	0.5289	-0.1388	-0.0729	-0.0339	0.0809	-0.0854	-0.1269	0.3089	29.4181	-30.4709	-64.2871
19	0	-2.2838	-0.2814	0.0191	19.2218	0	-0.1609	0.0795	-0.4525	-0.737	-0.0001	0.1535	2.3234	0.2201	0.161	-2.453	-0.6555	-0.1259	-0.3127	-0.0415	0.2217	21.3724	-31.0792	-58.5629
20	5.7651	0.2054	2.1951	4.2205	3.0497	8.7314	-0.0854	0.7051	-0.6929	-0.6492	0.2309	0.4686	1.2739	-0.6471	-0.1455	-0.2681	-0.0798	0.0503	-0.2162	-0.0935	0.3006	17.1185	-36.6211	-57.7185
21	0.3295	-1.1833	2.2367	0	-2.089	0.002	-0.0248	0.0268	0.2133	-0.08	0.17	-0.0946	-0.3255	-0.0385	-0.1452	-0.0506	0.1973	-0.1977	-0.0287	-0.1794	0.2741	28.6267	-20.9205	-49.1682
22	4.7218	-10.0699	3.1698	0.0006	0.5853	4.3171	-0.2802	-0.2157	-0.128	0.0896	-0.4223	0.0752	0.3795	-0.1759	0.7025	-0.1008	0.0993	0.198	-0.0723	0.0446	0.222	23.2778	-34.0364	-48.5463
23	10.5797	-3.1157	3.1178	0.0174	3.6258	0.609	0.1556	-0.1201	-0.7552	0.286	0.3767	-0.5693	0.9163	0.7811	-0.5323	-0.0395	0.0247	-0.0343	-0.0975	-0.2129	0.1911	30.6266	-31.4046	-53.5919
24	0.0031	2.6289	-0.1171	0.0028	3.5798	4.1057	0.0143	-0.0221	0.2795	-0.4836	0.1795	-0.2996	-0.0712	0.3223	-0.1938	-0.4242	0.0159	0.1263	0.1209	-0.0271	0.4848	33.4619	-29.2242	-60.373
25	4.9813	-4.7666	-1.6554	10.1382	5.9159	4.7594	0.0565	0.2032	-0.6846	0.1581	-0.0751	-0.1161	0.2711	0.0632	0.0186	-0.409	0.0016	-0.0187	-0.242	-0.0424	0.1022	20.9372	-32.3297	-56.7036
26	1.5799	-1.7715	-3.0745	9.8262	-0.2281	0.4464	-0.0521	0.5322	-0.3143	-0.4986	0.2132	-0.1057	-0.0324	-0.0387	-0.1611	-0.3422	-0.0174	-0.1429	-0.2677	-0.1455	-0.0242	20.2315	-31.2495	-63.7013
27	3.8535	0.9	10.703	0.0918	-0.9545	0.7439	-0.0604	0.3036	0.2937	-1.0289	-0.0154	0.9306	0.0393	-0.3421	0.0758	0.4271	0.0704	-0.4239	0.5674	0.0891	0.6428	12.674	-61.5845	-51.968
28	0.3862	1.5965	1.1676	5.3694	-4.7509	3.8765	0.008	0.5025	-0.0121	-1.0074	0.3681	0.0183	0.2037	-0.0375	-0.3761	0.2029	-0.099	-0.311	-0.07	-0.0327	0.0538	23.2969	-65.8586	-44.8625
29	6.9061	-0.7174	-0.8309	0.6264	3.6386	8.9847	-0.1819	-0.0879	0.3253	-0.4345	-0.1021	0.0254	-1.0015	-0.0273	0.284	-0.0329	-0.0428	-0.3353	0.1414	0.1347	0.5573	18.2755	-59.7909	-38.9188
30	1.814	-5.5371	6.0244	0.003	-0.597	1.4498	0.1107	-0.0353	-0.158	0.0246	-0.1596	0.2033	-0.8141	-0.483	0.049	-0.0576	-0.0578	-0.1741	0.445	0.2137	0.4383	12.6856	-60.8001	-34.5988
31	0.8846	-5.8244	-1.5811	0	-0.2528	0	0.0463	-0.0987	-0.0532	0.0112	0.0577	0.4069	0.2422	-0.642	-0.1041	0.1033	-0.0601	-0.36	0.2961	0.1123	1.0697	10.4165	-65.0683	-39.6346
32	0.8843	3.4085	0.9688	0.9187	0.6889	1.1971	-0.03	0.26	0.2742	-0.3589	0.2126	0.1651	0.7853	0.3447	-0.1826	0.6779	-0.087	-0.5909	0.492	-0.1325	0.9165	13.4784	-68.9745	-47.6175
33	2.0449	-1.4178	6.7098	0.5885	-0.0979	0	-0.0276	0.0179	-0.07	0.0482	0.1798	0.1586	-0.2649	-0.2256	-0.1522	0.4683	0.0227	-0.4099	0.4961	0.2881	1.529	5.533	-53.3634	-43.6802
34	6.9565	3.0266	2.4133	6.8145	-2.0252	6.3915	-0.0262	0.6275	0.0011	-0.8608	-0.0193	0.5017	-0.1093	-0.1342	0.0455	0.0574	0.0361	-0.1396	-0.0526	-0.0263	0.0636	23.9989	-61.2856	-39.6543
35	6.1855	-3.5572	1.3354	5.826	-2.6874	2.4684	0.1055	0.3636	0.1768	-1.1014	0.1263	0.3209	0.2924	-0.4383	-0.2318	0.0487	-0.0092	-0.1902	0.0361	0.1819	0.274	21.9871	-57.7408	-46.9832

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	{ A\|30 - A\|50 }
2	X-RAY DIFFRACTION	2	{ A\|51 - A\|83 }
3	X-RAY DIFFRACTION	3	{ A\|86 - A\|98 }
4	X-RAY DIFFRACTION	4	{ A\|99 - A\|142 }
5	X-RAY DIFFRACTION	5	{ A\|143 - A\|167 }
6	X-RAY DIFFRACTION	6	{ A\|168 - A\|194 }
7	X-RAY DIFFRACTION	7	{ A\|195 - A\|251 }
8	X-RAY DIFFRACTION	8	{ A\|252 - A\|291 }
9	X-RAY DIFFRACTION	9	{ B\|31 - B\|50 }
10	X-RAY DIFFRACTION	10	{ B\|51 - B\|98 }
11	X-RAY DIFFRACTION	11	{ B\|99 - B\|118 }
12	X-RAY DIFFRACTION	12	{ B\|119 - B\|142 }
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