PDB-5dub: Context-independent anti-hypusine antibody FabHpu98 in complex wi...

ID or keywords:

Entry

Database: PDB / ID: 5dub

Title

Context-independent anti-hypusine antibody FabHpu98 in complex with deoxyhypusine

Components

Fab Hpu98 Heavy chain
Fab Hpu98 Light chain
Peptide: GLY-5GG-GLY-ALA

Keywords

IMMUNE SYSTEM / deoxyhypusine /

antibody / FabHpu98 /

eIF5A

Function / homology

Immunoglobulins /

Immunoglobulin-like /

Sandwich / Mainly Beta

Function and homology information

Biological species

Oryctolagus cuniculus (rabbit)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2 Å

Authors

Zhai, Q. / Carter, P.J.

Citation

Journal: J.Mol.Biol. / Year: 2016
Title: Structural Analysis and Optimization of Context-Independent Anti-Hypusine Antibodies.
Authors: Zhai, Q. / He, M. / Song, A. / Deshayes, K. / Dixit, V.M. / Carter, P.J.

History

Deposition	Sep 18, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 20, 2016	Provider: repository / Type: Initial release
Revision 1.1	Feb 3, 2016	Group: Database references
Revision 1.2	Mar 2, 2016	Group: Database references
Revision 2.0	May 8, 2019	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence Category: citation / entity_poly ...citation / entity_poly / pdbx_struct_oper_list / pdbx_struct_special_symmetry Item: _citation.journal_id_CSD / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5dub.cif.gz	334.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5dub.ent.gz	285 KB	Display	PDB format
PDBx/mmJSON format	5dub.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/du/5dub ftp://data.pdbj.org/pub/pdb/validation_reports/du/5dub	HTTPS FTP

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Related structure data

Related structure data	5drnC 5ds8C 5dscC 5dtfC C: citing same article (ref.)
Similar structure data	6bpb-d 3eyo-2 2zkh-d 2bmk-1 7jwp-6 3dro-d 5tkk-d 6x1t-3 4tul-d 5yfi-d 1jgl-d 1f4y-d 1ct8-3 2gcy-d 1l7i-d 4xh2-5 6u3z-1 5b6f-3 4qxg-d 6u3z-2 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 - HomologyF&H Search

Related structure data

C: citing same article (ref.)

Similar structure data

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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)

Deposited unit

A: Fab Hpu98 Heavy chain

B: Fab Hpu98 Light chain

H: Fab Hpu98 Heavy chain

L: Fab Hpu98 Light chain

P: Peptide: GLY-5GG-GLY-ALA

hetero molecules

94.7 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Fab Hpu98 Heavy chain

B: Fab Hpu98 Light chain

hetero molecules

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

2

H: Fab Hpu98 Heavy chain

L: Fab Hpu98 Light chain

P: Peptide: GLY-5GG-GLY-ALA

hetero molecules

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

Unit cell

Length a, b, c (Å)	105.672, 293.976, 68.819
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	21
Space group name H-M	C222

Components on special symmetry positions

ID	Model	Components
1	1	A-305- SO4
2	1	H-307- SO4

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Protein/peptide , 1 types, 1 molecules P

#3: Protein/peptide	Peptide: GLY-5GG-GLY-ALA Mass: 402.490 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Antibody , 2 types, 4 molecules AHBL

#1: Antibody	Fab Hpu98 Heavy chain Mass: 23483.127 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody	Fab Hpu98 Light chain Mass: 22624.021 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Cricetulus griseus (Chinese hamster)

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Non-polymers , 3 types, 262 molecules

#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO₄
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.88 Å³/Da / Density % sol: 57.34 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, sitting drop / Details: 15% PEG8000 0.4M Li2SO4

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: RAYONIX MX300HS / Detector: CCD / Date: Mar 18, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2→43 Å / Num. obs: 74438 / % possible obs: 99.9 % / Redundancy: 7.1 % / Net I/σ(I): 16

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Processing

Software

Name	Version	Classification
HKL-2000		data scaling
PHENIX	1.8.2_1309	refinement
PDB_EXTRACT	3.15	data extraction
HKL-2000		data reduction

Refinement

Resolution: 2→43 Å / FOM work R set: 0.82 / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.68 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2196	3526	5.06 %
R_work	0.181	70673	-
obs	0.1829	74438	98.72 %

Solvent computation

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

Displacement parameters

B_iso max: 156.66 Å² / B_iso mean: 53.88 Å² / B_iso min: 26 Å²

Refinement step

Cycle: final / Resolution: 2→43 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6287	0	121	235	6643
B_iso mean	-	-	82.26	50.76	-
Num. residues	-	-	-	-	845

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	6556
X-RAY DIFFRACTION	f_angle_d	1.344	8939
X-RAY DIFFRACTION	f_chiral_restr	0.094	1055
X-RAY DIFFRACTION	f_plane_restr	0.006	1116
X-RAY DIFFRACTION	f_dihedral_angle_d	12.397	2263

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2-2.0019	0.3022	97	0.266	1813	1910	69
2.0019-2.0283	0.2939	146	0.254	2587	2733	100
2.0283-2.0561	0.2744	144	0.2417	2598	2742	100
2.0561-2.0854	0.2666	120	0.2301	2650	2770	100
2.0854-2.1166	0.2559	143	0.219	2594	2737	100
2.1166-2.1496	0.2615	137	0.2156	2614	2751	100
2.1496-2.1849	0.2873	151	0.2077	2601	2752	100
2.1849-2.2226	0.2501	128	0.2142	2646	2774	100
2.2226-2.263	0.2959	141	0.2147	2602	2743	100
2.263-2.3065	0.2731	148	0.2123	2644	2792	100
2.3065-2.3536	0.2422	136	0.2015	2605	2741	100
2.3536-2.4047	0.2611	129	0.1983	2653	2782	100
2.4047-2.4607	0.218	147	0.1954	2632	2779	100
2.4607-2.5222	0.2593	155	0.1963	2614	2769	100
2.5222-2.5904	0.2809	117	0.1931	2643	2760	100
2.5904-2.6666	0.2788	144	0.1934	2660	2804	100
2.6666-2.7527	0.2801	151	0.1994	2635	2786	100
2.7527-2.851	0.2841	129	0.202	2644	2773	100
2.851-2.9652	0.2499	151	0.2042	2619	2770	100
2.9652-3.1001	0.2269	148	0.2025	2671	2819	100
3.1001-3.2635	0.2356	147	0.1982	2647	2794	100
3.2635-3.4678	0.2238	136	0.1953	2671	2807	100
3.4678-3.7355	0.2111	124	0.1685	2685	2809	100
3.7355-4.1111	0.1748	129	0.1584	2705	2834	100
4.1111-4.7053	0.1489	140	0.1347	2697	2837	100
4.7053-5.9258	0.1858	162	0.1466	2722	2884	100
5.9258-42.9104	0.2121	165	0.1842	2821	2986	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	0.5261	0.2234	0.2167	0.1315	0.0689	0.0564	-0.1742	-0.3089	-0.2376	-0.0513	-0.0402	-0.1525	0.5948	0.3825	-0.0003	0.4639	0.0246	0.0081	0.4239	0.0076	0.4475	40.0831	122.6672	19.866
2	1.814	0.1576	0.0626	1.812	0.6274	0.635	0.0353	0.0673	-0.1434	-0.04	-0.0918	-0.0812	0.0431	0.0347	-0.0001	0.42	-0.0098	-0.0212	0.2864	0.0012	0.3328	29.3125	116.105	21.4443
3	0.7779	-0.4229	-0.017	0.5915	0.5146	0.634	0.0996	0.0308	-0.054	-0.0113	0.0014	0.1811	0.0811	-0.1562	0.0001	0.4364	-0.0333	-0.0007	0.3431	0.0046	0.3646	29.0868	123.4095	22.1791
4	1.0868	0.419	0.5838	0.508	0.0768	0.3051	-0.1385	-0.298	0.1108	-0.16	-0.0245	-0.2557	-0.3652	0.2299	-0.0179	0.4691	0.0262	0.01	0.3302	-0.0207	0.2859	41.9601	158.1342	20.2607
5	0.8741	0.2294	0.0916	0.7859	-0.4058	0.1986	-0.0556	-0.0362	-0.0782	0.0078	0.1333	0.0206	-0.0098	-0.3451	0.0001	0.4248	0.0007	0.004	0.4392	-0.0019	0.2638	38.8605	146.356	20.4378
6	0.5038	0.2316	0.1198	0.2629	-0.3336	0.7593	-0.049	0.0236	-0.129	0.3327	-0.189	-0.2268	-0.0346	-0.131	-0.0011	0.3533	-0.0056	-0.0131	0.296	-0.0251	0.2427	45.8198	151.736	25.6827
7	0.0542	-0.1144	0.4128	0.4412	0.0275	0.2635	0.2168	0.0322	-0.0602	-0.8601	-0.2298	0.4237	0.088	-0.335	-0.0014	0.4406	0.0114	-0.132	0.5096	-0.0842	0.5282	9.2359	132.6088	18.7237
8	0.6495	-0.5999	-0.0847	0.4705	-0.0646	0.616	0.17	-0.1062	-0.3227	-0.0031	-0.2462	0.2132	0.2886	-0.1948	0	0.4313	-0.0891	-0.0661	0.3813	-0.0584	0.5036	11.4095	121.5399	23.3531
9	0.5913	-0.629	0.1893	0.5165	0.1446	0.5838	-0.0935	-0.1027	0.1071	0.2755	0.0191	-0.0318	0.2068	0.0058	-0.0002	0.3575	-0.051	0.0129	0.3879	-0.021	0.4151	15.6611	129.5488	32.0921
10	0.5017	-0.0093	-0.2596	1.0389	-0.6421	0.1497	0.1201	0.0932	0.0057	-0.5155	-0.1766	0.3945	-0.0791	-0.1456	-0	0.3646	-0.0288	-0.0805	0.3536	-0.0498	0.4005	12.4184	127.8803	23.1858
11	0.0106	0.12	-0.0376	0.1051	-0.0443	-0.0123	0.0685	0.1181	-0.0345	-0.2521	0.0394	0.4735	-0.028	0.0472	-0.0002	0.4458	0.0513	-0.0079	0.4269	-0.0035	0.4208	14.9554	149.3892	23.1953
12	0.0941	0.042	0.1002	0.1963	0.1216	0.1413	-0.0006	-0.1507	0.0383	-0.0062	-0.151	-0.0684	0.0287	0.4755	0.0003	0.3905	0.0366	0.0287	0.4845	0.0765	0.3778	41.0576	159.2954	13.0353
13	0.8016	-0.281	-0.1714	0.4605	-0.1162	0.1684	0.1234	0.3652	0.0802	-0.2054	-0.0501	0.1469	0.018	-0.221	-0	0.38	0.0305	-0.0145	0.4495	0.025	0.2717	28.3334	156.4289	10.535
14	1.151	-0.6323	0.5187	0.3327	-0.2782	0.1064	0.0571	0.1738	-0.0194	-0.1322	-0.165	0.1854	0.0129	-0.1312	-0.0077	0.3859	0.0077	-0.0169	0.3541	0.012	0.2646	30.5728	153.3231	14.8146
15	1.447	0.552	-0.4221	1.0924	-0.0361	0.4507	0.3543	0.4138	1.2609	-0.4729	-0.3111	0.4785	0.0351	-0.0875	-0.1045	0.4973	0.1676	0.0504	0.5654	0.2229	0.503	28.3795	163.8459	8.1428
16	0.229	-0.3978	0.1161	0.5193	-0.5361	0.65	0.2882	-0.1076	0.8856	-0.2414	-0.3305	-0.2016	-0.5334	0.5025	-0.0358	0.5059	0.0276	-0.0026	0.3849	0.1208	0.6254	33.2209	167.6161	11.3602
17	0.2531	0.1708	0.1833	0.0824	0.013	0.1406	-0.0989	0.2481	-0.7195	0.1303	0.3016	0.7737	0.1742	-0.4309	0.0006	0.5094	-0.0442	0.0683	0.5422	-0.0562	0.723	10.197	93.6919	24.353
18	1.9971	-0.6815	1.0044	1.0019	0.711	1.5906	-0.1716	-0.0949	-0.3003	0.6325	0.106	0.1668	-0.0636	-0.139	-0	0.5722	-0.0241	0.1143	0.349	0.0262	0.504	20.1779	90.5862	31.6279
19	0.7163	0.3021	0.2769	0.5271	0.3453	0.3784	-0.1717	0.1207	-0.0932	0.2478	-0.0234	-0.1681	-0.0935	-0.1388	-0.0015	0.4237	-0.0281	0.0344	0.3443	-0.0265	0.5316	21.2461	91.2635	24.2369
20	1.6063	0.4442	0.0444	0.4251	-0.5462	0.7011	-0.0296	0.0491	-0.0331	-0.092	0.0288	-0.0262	-0.1269	0.1788	-0	0.4246	0.0339	0.0074	0.6141	-0.1424	0.4715	12.8628	95.8071	-2.0239
21	0.2437	0.0123	0.0251	0.3253	-0.2731	0.2073	-0.041	0.0359	-0.3917	0.1886	0.4092	-0.048	0.412	-0.184	0.0681	0.3944	-0.0182	0.0095	0.6822	-0.177	0.5276	6.6927	90.304	-3.8761
22	0.4077	0.0177	-0.1205	0.5506	-0.1648	0.5317	0.0084	0.2425	0.0089	0.4218	-0.22	-0.6051	-0.1679	0.3721	-0.0513	0.3835	-0.0936	-0.0323	0.5383	0.1168	0.6869	40.4238	92.9949	21.9173
23	0.184	-0.2332	-0.2354	0.3164	0.0175	0.5148	0.1582	0.5617	-0.214	-0.1999	-0.3119	-0.343	0.2621	0.3633	0.0001	0.3931	0.0424	0.0279	0.6065	-0.007	0.6338	38.7456	84.6652	19.0544
24	0.3274	-0.3132	0.0635	0.1481	-0.1771	0.0524	0.2134	0.4919	0.0799	0.1666	-0.2662	-0.6124	0.654	0.3745	-0.0007	0.5281	0.0892	0.0614	0.6497	0.0189	0.6018	36.6887	89.088	13.4046
25	0.0691	0.0178	-0.097	0.0044	-0.0972	0.0741	-0.3232	0.0748	0.0201	0.6359	0.1976	-0.4312	-0.923	-0.0486	-0.0003	0.6594	-0.0286	-0.0568	0.3995	0.0302	0.5917	32.5378	95.0675	31.7016
26	0.1196	0.2994	0.0171	0.2618	-0.2882	0.2265	0.1575	0.7234	0.0078	-0.2306	-0.3361	0.025	0.2349	0.7933	0.0005	0.5804	0.1059	0.1201	1.0515	0.0268	0.6059	32.3379	96.1981	-4.3189
27	0.0406	0.0328	0.0771	0.0396	-0.034	0.2189	0.0513	0.4972	0.292	0.0258	0.0499	-0.0579	-0.3599	-0.2988	-0.0001	0.5929	0.1435	0.0614	1.0393	0.1392	0.6366	11.3061	105.1997	-8.8398
28	0.0388	-0.077	-0.075	0.0524	-0.0717	-0.0096	-0.3986	0.0733	0.4056	0.1639	0.6551	0.1452	-0.7506	0.8555	0.0013	0.685	-0.0713	0.1127	1.0437	0.128	0.8945	29.1589	104.1264	-7.7391
29	0.0079	-0.055	0.0532	0.0453	-0.0446	0.0168	-0.1419	0.2398	0.0723	-0.4416	0.4012	0.3528	0.0766	0.0878	0.0001	0.7174	-0.1536	0.1186	0.7768	0.0723	0.776	22.0491	111.8826	-5.6989
30	0.0111	-0.0242	-0.0207	0.0203	0.0125	-0.0122	-0.1784	0.605	0.3596	-0.5749	0.1217	-0.5328	-0.0893	0.6663	-0	0.5017	0.0449	0.043	0.976	-0.0475	0.5604	31.1444	91.3537	-1.1157
31	0.0167	0.0256	-0.0575	0.0339	-0.11	0.0992	0.1796	0.5982	0.3701	0.0212	-0.0766	0.4147	-0.7424	0.3493	-0.0001	0.8466	-0.0079	-0.014	0.7981	0.1723	0.8083	13.5901	111.3747	-7.897
32	0.132	0.2503	-0.0233	0.3534	0.007	0.0965	-0.4508	0.3245	0.4423	-0.0453	0.0377	-0.0004	-0.9021	0.2006	-0.0014	0.7923	-0.0222	0.0287	1.2512	0.3073	0.8042	23.0257	108.7596	-15.6989
33	0.1572	-0.1258	0.0575	0.0706	-0.0128	0.059	0.6269	-0.2594	-0.2167	0.418	0.31	-0.4885	-0.0299	0.0076	0.0005	0.8039	-0.0167	-0.0765	0.4683	0.0108	0.8341	37.4093	83.5203	38.9782

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 22 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 23 through 82 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 82A through 116 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 117 through 140 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 141 through 180 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 181 through 210 )	A
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1 through 25 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 26 through 38 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 39 through 61 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 62 through 101 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 102 through 113 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 114 through 128 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 129 through 162 )	B
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 163 through 186 )	B
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 187 through 199 )	B
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 200 through 211 )	B
17	X-RAY DIFFRACTION	17	chain 'H' and (resid 3 through 22 )	H
18	X-RAY DIFFRACTION	18	chain 'H' and (resid 23 through 82 )	H
19	X-RAY DIFFRACTION	19	chain 'H' and (resid 82A through 116 )	H
20	X-RAY DIFFRACTION	20	chain 'H' and (resid 117 through 181 )	H
21	X-RAY DIFFRACTION	21	chain 'H' and (resid 182 through 210 )	H
22	X-RAY DIFFRACTION	22	chain 'L' and (resid 1 through 38 )	L
23	X-RAY DIFFRACTION	23	chain 'L' and (resid 39 through 75 )	L
24	X-RAY DIFFRACTION	24	chain 'L' and (resid 76 through 90 )	L
25	X-RAY DIFFRACTION	25	chain 'L' and (resid 91 through 101 )	L
26	X-RAY DIFFRACTION	26	chain 'L' and (resid 102 through 118 )	L
27	X-RAY DIFFRACTION	27	chain 'L' and (resid 119 through 137 )	L
28	X-RAY DIFFRACTION	28	chain 'L' and (resid 138 through 149 )	L
29	X-RAY DIFFRACTION	29	chain 'L' and (resid 150 through 162 )	L
30	X-RAY DIFFRACTION	30	chain 'L' and (resid 163 through 173 )	L
31	X-RAY DIFFRACTION	31	chain 'L' and (resid 174 through 186 )	L
32	X-RAY DIFFRACTION	32	chain 'L' and (resid 187 through 208 )	L
33	X-RAY DIFFRACTION	33	chain 'P' and (resid 3 through 6 )	P

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