PDB-5ds8: Context-independent anti-hypusine antibody FabHpu98 in complex wi...

ID or keywords:

Entry

Database: PDB / ID: 5ds8

Title

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

Components

Fab Hou98 Light Chain
Fab Hpu98 Heavy Chain
Tetrapeptide GLY-HPU-GLY-ALA

Keywords

IMMUNE SYSTEM / hypusine / 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 /

MOLECULAR REPLACEMENT / Resolution: 1.95 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 17, 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: Derived calculations
Revision 1.2	Mar 2, 2016	Group: Database references
Revision 1.3	May 4, 2016	Group: Non-polymer description
Revision 2.0	Feb 19, 2020	Group: Derived calculations / Polymer sequence / Category: entity_poly / pdbx_struct_oper_list Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_oper_list.symmetry_operation
Revision 2.1	Sep 27, 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2	Nov 15, 2023	Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag
Revision 2.3	Oct 30, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5ds8.cif.gz	335.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5ds8.ent.gz	274.9 KB	Display	PDB format
PDBx/mmJSON format	5ds8.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5ds8_validation.pdf.gz	491.7 KB	Display	wwPDB validaton report
Full document	5ds8_full_validation.pdf.gz	499.5 KB	Display
Data in XML	5ds8_validation.xml.gz	33.3 KB	Display
Data in CIF	5ds8_validation.cif.gz	47.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ds/5ds8 ftp://data.pdbj.org/pub/pdb/validation_reports/ds/5ds8	HTTPS FTP

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Related structure data

Related structure data	5drnSC 5dscC 5dtfC 5dubC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4xbg-3 1mfd-d 4r4b-4 4xcy-5 1ejo-d 3qg7-d 6dwi-5 4lly-1 1c5d-3 6xrj-1 1ngx-2 4xcy-6 4r7d-1 5h2b-d 1kfa-1 6obz-1 4xbg-4 3eo0-2 4ocy-d 3ra7-2 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

5drnSC

5dscC

5dtfC

5dubC

S: Starting model for refinement

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 Hou98 Light Chain

H: Fab Hpu98 Heavy Chain

L: Fab Hou98 Light Chain

P: Tetrapeptide GLY-HPU-GLY-ALA

hetero molecules

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

1

A: Fab Hpu98 Heavy Chain

B: Fab Hou98 Light Chain

hetero molecules

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

2

H: Fab Hpu98 Heavy Chain

L: Fab Hou98 Light Chain

P: Tetrapeptide GLY-HPU-GLY-ALA

hetero molecules

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

Unit cell

Length a, b, c (Å)	106.005, 294.085, 68.737
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-476- HOH

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Protein/peptide , 1 types, 1 molecules P

#3: Protein/peptide	Tetrapeptide GLY-HPU-GLY-ALA Mass: 418.489 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Synthemis (insect)

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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 Hou98 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, 258 molecules

#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.89 Å³/Da / Density % sol: 57.39 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 20% PEG8000 0.5M Li2SO4 15.7mg/ml

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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: MARMOSAIC 300 mm CCD / 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: 1.95→41.2 Å / Num. obs: 78566 / % possible obs: 99.8 % / Redundancy: 7.4 % / R_sym value: 0.075 / Net I/σ(I): 22
Reflection shell	Resolution: 1.95→2.02 Å / Redundancy: 6.5 % / R_merge(I) obs: 0.851 / Mean I/σ(I) obs: 2.2 / % possible all: 99.9

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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
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5DRN

5drn

Resolution: 1.95→41.2 Å / FOM work R set: 0.8319 / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.65 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2235	3971	5.06 %
R_work	0.1827	74432	-
obs	0.1847	78403	99.64 %

Solvent computation

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

Displacement parameters

B_iso max: 131.15 Å² / B_iso mean: 49.44 Å² / B_iso min: 19.92 Å²

Refinement step

Cycle: final / Resolution: 1.95→41.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6239	0	74	242	6555
B_iso mean	-	-	60.94	45.63	-
Num. residues	-	-	-	-	837

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.014	6486
X-RAY DIFFRACTION	f_angle_d	1.496	8868
X-RAY DIFFRACTION	f_chiral_restr	0.122	1052
X-RAY DIFFRACTION	f_plane_restr	0.007	1111
X-RAY DIFFRACTION	f_dihedral_angle_d	12.734	2248

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.9503-1.9741	0.3091	126	0.2703	2497	2623	94
1.9741-1.9991	0.2781	149	0.2406	2576	2725	99
1.9991-2.0254	0.2461	148	0.223	2651	2799	100
2.0254-2.0532	0.2463	150	0.2227	2590	2740	100
2.0532-2.0825	0.2439	122	0.2153	2714	2836	100
2.0825-2.1136	0.2468	133	0.2043	2577	2710	100
2.1136-2.1466	0.2512	148	0.2072	2667	2815	100
2.1466-2.1818	0.2775	159	0.2023	2596	2755	100
2.1818-2.2194	0.2323	127	0.2102	2677	2804	100
2.2194-2.2598	0.2779	136	0.1916	2634	2770	100
2.2598-2.3032	0.2408	147	0.2003	2658	2805	100
2.3032-2.3502	0.2305	142	0.196	2618	2760	100
2.3502-2.4013	0.2773	123	0.1926	2670	2793	100
2.4013-2.4572	0.2387	153	0.1923	2632	2785	100
2.4572-2.5186	0.2572	151	0.1925	2658	2809	100
2.5186-2.5867	0.2544	122	0.1926	2675	2797	100
2.5867-2.6628	0.2715	148	0.1894	2645	2793	100
2.6628-2.7487	0.2553	147	0.1962	2667	2814	100
2.7487-2.847	0.2902	139	0.21	2669	2808	100
2.847-2.9609	0.2365	152	0.2029	2641	2793	100
2.9609-3.0956	0.233	147	0.202	2669	2816	100
3.0956-3.2588	0.2428	146	0.1994	2664	2810	100
3.2588-3.4628	0.2188	135	0.1928	2700	2835	100
3.4628-3.7301	0.218	127	0.1742	2701	2828	100
3.7301-4.1051	0.1931	131	0.1647	2716	2847	100
4.1051-4.6984	0.1551	140	0.1374	2721	2861	100
4.6984-5.9167	0.2016	161	0.1518	2729	2890	100
5.9167-41.1888	0.2279	162	0.1948	2820	2982	98

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	0.1473	0.5539	0.1091	0.749	-0.0932	0.2615	-0.018	-0.3698	-0.1892	0.1626	-0.059	-0.3527	0.5709	0.3425	0.0002	0.4118	0.0102	-0.0086	0.3744	0.0124	0.3585	40.231	122.6913	19.858
2	2.2926	0.0531	0.1487	2.8285	0.9318	1.055	0.0739	0.062	-0.1437	-0.0812	-0.1066	-0.085	0.1736	-0.0045	-0.0001	0.3509	-0.0147	-0.0367	0.2309	0.011	0.2874	29.454	116.1153	21.4376
3	1.4674	-0.4862	-0.3762	0.9551	0.9214	1.6661	-0.0032	0.0028	-0.2545	-0.0183	-0.0341	0.1534	0.1542	-0.2517	0.0003	0.3628	-0.0169	-0.0128	0.2848	0.0058	0.3281	29.1873	123.4855	22.0709
4	1.6063	0.6388	0.8316	0.3195	-0.0456	0.9455	-0.2204	-0.2375	0.0837	-0.3991	-0.0068	-0.0223	-0.4326	0.0407	-0.0056	0.4103	0.056	-0.0204	0.2573	-0.0061	0.2379	42.4064	156.1615	19.6684
5	1.3965	0.0788	-0.0996	1.8176	-1.1121	0.5586	-0.036	0.0207	-0.1013	-0.0716	0.0999	0.202	0.044	-0.3447	0.0003	0.288	0.0011	-0.0035	0.3234	0.0026	0.1863	38.7825	146.6565	20.6127
6	2.0197	0.3567	0.6376	0.4176	-0.5399	1.1945	-0.1342	-0.0586	0.1785	0.5897	-0.0213	-0.289	-0.1508	-0.0918	0.0003	0.3726	0.0318	-0.0093	0.2681	-0.0107	0.1924	46.8093	151.5797	25.7959
7	-0.1981	-0.585	0.8088	1.851	0.3957	0.1858	0.1195	-0.0664	-0.0478	-0.7796	-0.174	0.3974	0.2364	-0.377	-0.0509	0.3702	0.0134	-0.1076	0.4395	-0.0715	0.4123	9.4346	132.7157	18.6156
8	0.9793	-1.0215	0.3758	0.9348	-0.3246	1.0261	0.3465	-0.1	-0.0475	0.315	-0.2667	0.3908	0.5059	-0.3382	0.0026	0.3218	-0.097	-0.0773	0.3386	-0.0378	0.3537	11.549	121.7178	23.1865
9	0.8939	-0.7927	0.2941	0.5205	0.257	0.8383	0.0469	-0.0966	0.1818	0.349	-0.0432	0.038	0.1538	0.0951	0	0.2681	-0.0664	-0.0041	0.3404	0.0014	0.3548	15.7677	129.6045	32.0086
10	0.3048	-0.3126	0.2464	0.8436	-0.8874	1.2394	0.1719	0.0406	0.0141	-0.2915	-0.2349	0.4094	0.0162	-0.0899	0.0001	0.2845	-0.0312	-0.0511	0.3222	-0.0707	0.4223	10.5301	132.1172	25.8199
11	0.326	0.0585	0.0226	0.6996	0.2867	0.0988	-0.1341	0.0092	-0.0155	-1.2746	0.1268	0.3167	0.0969	-0.47	0.003	0.512	-0.0275	-0.1463	0.3554	-0.0549	0.3953	17.1056	118.1872	16.3648
12	-0.0042	0.3082	-0.2452	0.2235	-0.3211	0.3023	0.1695	0.0705	0.0523	-0.085	-0.0389	0.2001	-0.0142	-0.0426	0.0001	0.3254	0.0292	-0.0051	0.3505	0.0075	0.3719	15.1074	149.4703	23.2663
13	0.2118	-0.0951	0.1237	0.1262	-0.0347	0.0729	-0.0474	0.2015	0.3666	0.0851	-0.0535	0	0.1137	0.0503	-0.0003	0.3498	0.0211	0.0477	0.3975	0.0599	0.3061	41.2171	159.3986	13.0531
14	2.3114	-0.4844	-0.6676	0.339	0.2253	0.3567	0.038	0.2337	0.1234	-0.1586	-0.0566	0.1579	0.0958	-0.0765	0.0001	0.3287	0.0189	-0.0191	0.3545	0.0144	0.2486	26.6993	154.6195	14.4326
15	0.9592	-0.7956	-0.0906	0.4441	-0.1856	0.4003	-0.1973	1.2731	0.1906	-0.2726	0.1909	-0.0746	0.6014	-0.9003	-0.0012	0.3671	0.068	0.0102	0.4217	0.085	0.2322	38.436	157.2097	5.4359
16	2.2144	0.4717	-0.8749	1.5927	-1.3415	0.3381	0.1338	0.4241	1.4946	-0.3436	-0.1084	0.4105	-0.0177	-0.1056	-0.1122	0.4212	0.0939	0.0077	0.4141	0.1666	0.4357	29.4158	165.1569	9.5767
17	0.3926	0.2777	0.0597	0.2964	-0.2023	0.2964	-0.1261	0.0922	-0.7335	0.1569	0.1867	1.145	0.296	-0.3445	-0.0008	0.4648	-0.0331	0.0773	0.5015	-0.0349	0.6328	10.2374	93.8671	24.254
18	2.2818	-1.0199	0.7074	1.2429	0.8807	1.4981	-0.0933	-0.1156	-0.3682	0.6213	0.0282	-0.0279	-0.0896	0.1165	0.0001	0.4782	-0.0418	0.037	0.2855	0.0302	0.4825	22.7368	89.4905	30.6964
19	2.5639	-0.2883	1.093	1.6784	0.2235	1.5015	-0.1668	0.0347	-0.3395	0.5086	-0.0143	0.1802	-0.0977	-0.1512	0	0.428	-0.0429	0.0851	0.293	0.0021	0.4737	19.2307	91.8603	27.1835
20	2.8128	1.2313	0.6085	1.5424	-1.1602	2.2529	-0.0276	0.217	-0.1588	-0.3472	-0.0244	-0.2256	-0.3333	0.4216	0.0003	0.3376	0.0283	0.016	0.6343	-0.1343	0.4733	12.8256	95.7643	-1.7585
21	0.5226	-0.2845	-0.325	0.9106	0.0707	0.1901	-0.1077	0.2026	-0.6381	-0.192	0.1706	0.5551	-0.1338	0.5938	0.0685	0.4267	0.0197	-0.0732	0.7975	-0.2804	0.6096	8.4557	89.2853	-4.8477
22	0.766	0.2085	0.0656	-0.0248	-0.0125	0.109	-0.0815	0.0252	-0.4487	-0.0736	0.4041	0.0764	0.5074	0.3803	0.0007	0.444	0.0131	-0.0077	0.6729	-0.0606	0.4483	3.7486	92.394	-0.8314
23	0.3914	-0.3686	0.1969	0.6642	-0.1393	0.724	-0.0642	0.3101	0.0988	0.5206	-0.2397	-0.5444	-0.1676	0.6046	-0.0408	0.3622	-0.1265	-0.0468	0.6147	0.1463	0.6485	40.456	93.0749	21.7222
24	1.9025	-1.719	0.4714	2.119	-1.4156	1.8313	0.1027	0.4456	-0.0623	0.0929	-0.3427	-0.3514	-0.102	0.4203	-0.0006	0.2724	-0.0149	0.0273	0.503	0.0161	0.5649	37.0905	87.8988	20.0392
25	0.2027	0.7759	-0.2055	2.2872	-0.8052	0.8312	-0.1249	1.1436	-0.2616	0.0367	-0.7409	-0.5116	0.3488	0.0602	-0.5705	0.2566	0.1267	0.1987	1.4212	0.0273	0.5769	37.6733	94.7771	-0.1533
26	0.3732	0.6561	-0.0326	0.7842	-0.2061	3.6613	0.1095	0.6225	0.3379	-0.1232	-0.2213	-0.0755	-0.5841	0.3254	-0.0003	0.5406	-0.0388	0.0409	0.9129	0.1157	0.6311	21.26	105.6165	-9.2125
27	0.1825	-0.0396	0.017	-0.0051	0.0323	0.0326	1.2074	-0.3341	-0.1648	0.7955	0.1168	-0.98	-0.4723	0.1522	0.0052	0.697	-0.0001	-0.1944	0.509	0.1422	0.8955	37.4249	83.8525	38.663

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 83A through 116 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 117 through 142 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 143 through 182 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 183 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 90 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 91 through 101 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 102 through 113 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 114 through 128 )	B
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 129 through 173 )	B
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 174 through 186 )	B
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 187 through 208 )	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 62 )	H
19	X-RAY DIFFRACTION	19	chain 'H' and (resid 63 through 116 )	H
20	X-RAY DIFFRACTION	20	chain 'H' and (resid 117 through 183 )	H
21	X-RAY DIFFRACTION	21	chain 'H' and (resid 184 through 197 )	H
22	X-RAY DIFFRACTION	22	chain 'H' and (resid 198 through 210 )	H
23	X-RAY DIFFRACTION	23	chain 'L' and (resid 1 through 38 )	L
24	X-RAY DIFFRACTION	24	chain 'L' and (resid 39 through 101 )	L
25	X-RAY DIFFRACTION	25	chain 'L' and (resid 102 through 113 )	L
26	X-RAY DIFFRACTION	26	chain 'L' and (resid 114 through 208 )	L
27	X-RAY DIFFRACTION	27	chain 'P' and (resid 3 through 6 )	P

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