PDB-5drn: Context-independent anti-hypusine antibody FabHpu24 in complex wi...

ID or keywords:

Entry

Database: PDB / ID: 5drn

Title

Context-independent anti-hypusine antibody FabHpu24 in complex with hypusine

Components

Fab Hpu24 Heavy chain
Fab Hpu24 Light chain

Keywords

IMMUNE SYSTEM / hypusine / antibody / FabHpu24 / eIF5A

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Hypusine

Function and homology information

Biological species

Oryctolagus cuniculus (rabbit)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.994 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 16, 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 1.3	May 4, 2016	Group: Non-polymer description
Revision 2.0	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_initial_refinement_model / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_oper_list.symmetry_operation
Revision 2.1	Nov 15, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5drn.cif.gz	337.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5drn.ent.gz	275.1 KB	Display	PDB format
PDBx/mmJSON format	5drn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5drn_validation.pdf.gz	466 KB	Display	wwPDB validaton report
Full document	5drn_full_validation.pdf.gz	469.7 KB	Display
Data in XML	5drn_validation.xml.gz	34.6 KB	Display
Data in CIF	5drn_validation.cif.gz	49.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dr/5drn ftp://data.pdbj.org/pub/pdb/validation_reports/dr/5drn	HTTPS FTP

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Related structure data

Related structure data	5ds8C 5dscC 5dtfC 5dubC 4hbcS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5mvj-2 4jzo-2 1rul-d 4p3c-d 5u15-1 4jn2-2 4yhi-1 6x1v-d 1mjj-1 4jn1-d 5alb-d 5mu2-6 6wwc-2 5dqj-2 4k23-d 5erw-d 6rlm-3 7jwq-1 6qn8-3 5lgh-d 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.)

S: Starting model for refinement

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 Hpu24 Heavy chain

B: Fab Hpu24 Light chain

H: Fab Hpu24 Heavy chain

L: Fab Hpu24 Light chain

hetero molecules

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

1

A: Fab Hpu24 Heavy chain

B: Fab Hpu24 Light chain

hetero molecules

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

2

H: Fab Hpu24 Heavy chain

L: Fab Hpu24 Light chain

hetero molecules

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

Unit cell

Length a, b, c (Å)	42.453, 167.350, 68.326
Angle α, β, γ (deg.)	90.000, 98.930, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Antibody	Fab Hpu24 Heavy chain Mass: 22833.768 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 Hpu24 Light chain Mass: 22685.896 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)
#3: Chemical	ChemComp-5CT / Hypusine / N~6~-[(2S)-4-amino-2-hydroxybutyl]-L-lysine Type: peptide linking / Mass: 233.308 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₂₃N₃O₃
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 354 / 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: 2.63 Å³/Da / Density % sol: 53.3 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20% PEG3350 0.1M Bis-Tris Propane pH7.0 0.2M K.Na phosphate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00001 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 15, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.00001 Å / Relative weight: 1
Reflection	Resolution: 1.9→43 Å / Num. obs: 63449 / % possible obs: 99.99 % / Redundancy: 3.8 % / R_sym value: 0.066 / Net I/σ(I): 30.7
Reflection shell	Resolution: 1.9→2 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.54 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4HBC

4hbc

Resolution: 1.994→43 Å / FOM work R set: 0.8058 / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.06 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2218	3230	5.09 %	Random selection
R_work	0.1832	60219	-	-
obs	0.1852	63449	99.31 %	-

Solvent computation

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

Displacement parameters

B_iso max: 180.12 Å² / B_iso mean: 34.05 Å² / B_iso min: 13.95 Å²

Refinement step

Cycle: final / Resolution: 1.994→43 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6356	0	54	354	6764
B_iso mean	-	-	44.01	35.9	-
Num. residues	-	-	-	-	857

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	6580
X-RAY DIFFRACTION	f_angle_d	1.368	8983
X-RAY DIFFRACTION	f_chiral_restr	0.094	1063
X-RAY DIFFRACTION	f_plane_restr	0.006	1134
X-RAY DIFFRACTION	f_dihedral_angle_d	13.073	2297

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.9942-2.0239	0.2741	139	0.2094	2434	2573	92
2.0239-2.0556	0.2963	132	0.2083	2593	2725	99
2.0556-2.0893	0.3088	149	0.2042	2600	2749	100
2.0893-2.1253	0.2464	153	0.2024	2665	2818	100
2.1253-2.1639	0.2829	126	0.1891	2574	2700	100
2.1639-2.2056	0.2497	124	0.1926	2682	2806	100
2.2056-2.2506	0.317	141	0.2333	2607	2748	100
2.2506-2.2995	0.2728	128	0.2267	2596	2724	99
2.2995-2.353	0.2523	150	0.2069	2676	2826	100
2.353-2.4118	0.2559	148	0.207	2582	2730	100
2.4118-2.477	0.2538	147	0.1985	2627	2774	99
2.477-2.5499	0.3096	136	0.2068	2609	2745	100
2.5499-2.6322	0.2325	114	0.1996	2667	2781	100
2.6322-2.7263	0.2363	152	0.1933	2591	2743	100
2.7263-2.8354	0.273	149	0.2165	2674	2823	100
2.8354-2.9644	0.2637	151	0.2065	2603	2754	100
2.9644-3.1207	0.2293	135	0.2068	2619	2754	100
3.1207-3.3161	0.2124	146	0.1925	2631	2777	100
3.3161-3.5721	0.2084	159	0.1779	2638	2797	100
3.5721-3.9313	0.1722	132	0.1686	2600	2732	98
3.9313-4.4997	0.1588	142	0.1408	2623	2765	100
4.4997-5.6671	0.1716	140	0.1384	2656	2796	100
5.6671-43.0093	0.1891	137	0.1714	2672	2809	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	0.2828	0.0124	-0.1136	0.1742	0.0243	0.4219	-0.0855	0.0874	-0.0577	-0.0513	0.0222	-0.049	-0.3098	-0.0011	-0.0034	0.4247	0.0116	-0.0419	0.2285	0.0143	0.2038	2.5529	-13.4775	-14.3363
2	0.2367	0.1791	-0.0209	0.7506	0.3753	0.3009	0.0934	-0.0736	-0.0091	-0.0056	-0.027	-0.0185	-0.0449	-0.1264	0.0003	0.1416	0.0121	-0.0215	0.2375	0.026	0.2393	-8.6234	-22.4129	15.1615
3	0.081	-0.0205	-0.0454	0.0486	0.0532	0.0563	-0.2451	0.0884	-0.0152	-0.1673	0.0913	-0.1335	0.129	-0.1382	-0.0003	0.3782	-0.0473	-0.0436	0.3073	-0.0058	0.2082	-2.3786	-39.2854	-16.6519
4	0.0475	-0.0523	0.0218	0.0355	-0.0139	0.0204	-0.0815	-0.0274	-0.0643	-0.1781	0.0608	0.0144	-0.1042	-0.0274	-0.0001	0.3731	-0.0588	0.0064	0.194	0.0022	0.1798	5.4975	-30.0573	-23.2594
5	0.1189	0.1015	-0.0451	0.2377	-0.0016	0.0389	-0.0948	-0.0084	-0.0578	-0.1198	0.067	-0.0377	-0.0314	0.0172	0	0.326	-0.022	-0.0101	0.2245	-0.0138	0.2044	6.476	-33.5481	-15.4311
6	0.0221	0.0247	-0.0104	0.0302	-0.0305	0.0194	-0.0109	0.1004	-0.1247	-0.0571	-0.0261	0.2008	-0.0949	-0.1319	-0.0001	0.251	-0.0468	-0.0456	0.2435	0.0159	0.2249	-2.741	-34.4079	-12.5925
7	0.0992	0.1294	-0.0083	0.3056	-0.3126	0.6521	0.0789	-0.2342	0.1971	-0.1222	0.2036	-0.076	0.2102	-0.1667	0.2321	0.0672	0.041	-0.0202	0.3107	0.0175	0.317	-16.5979	-31.1741	15.1207
8	0.1484	-0.0829	0.2039	1.1579	-0.2236	0.3424	-0.0352	0.048	0.1597	-0.7612	0.2246	0.1235	0.2416	-0.0902	0.1775	0.0118	0.0211	-0.1489	0.3216	0.0117	0.3032	-18.2555	-34.0726	8.3815
9	0.0535	0.1384	-0.1747	0.3911	-0.5586	0.7889	-0.0962	-0.1451	-0.0291	-0.0794	0.2534	0.3151	0.2425	-0.2828	0.1676	0.0423	0.0463	-0.0282	0.3801	0.0516	0.3498	-23.2478	-38.3345	16.5001
10	0.0363	0.0379	-0.012	0.0682	-0.0627	0.0936	0.0964	-0.0443	0.0079	-0.2335	-0.0162	-0.1705	0.4151	-0.0083	0.0019	0.3315	-0.0984	0.0319	0.2677	-0.0079	0.2792	1.1737	-84.4926	-28.0756
11	0.0325	0.0208	-0.0611	0.2964	0.1095	0.1445	-0.0906	-0.0673	-0.0632	0.0091	0.0316	-0.007	0.0776	-0.0578	0	0.1974	-0.0358	0.0309	0.2018	0.0045	0.2277	2.631	-80.9746	-16.3516
12	0.0042	-0.0079	-0.0168	0.176	0.1666	0.1677	-0.1582	-0.0355	0.0401	0.0626	0.0586	-0.0547	0.3813	-0.0668	-0.0009	0.2722	-0.1037	0.054	0.252	0.0325	0.3202	-5.672	-84.3062	-22.8972
13	0.066	-0.0389	-0.0284	0.2291	0.0134	0.013	-0.1069	-0.0601	0.016	0.278	0.1083	0.0222	-0.0448	-0.0878	-0.0044	0.2108	-0.0441	0.01	0.2225	-0.0007	0.2687	7.6502	-75.4241	-14.6263
14	0.2924	-0.1515	-0.0009	0.1073	0.0145	0.039	-0.1141	-0.0778	-0.0694	-0.3876	0.0888	-0.1708	0.238	-0.0289	-0.0541	0.3596	-0.1267	-0.0077	0.2724	0.0012	0.2756	-1.5953	-79.939	-32.5447
15	0.0369	-0.0457	-0.0016	0.0388	-0.0086	0.0004	0.3456	0.3529	0.2453	-0.1553	-0.0606	-0.1154	0.1194	0.009	0.0025	0.7044	-0.068	0.0846	0.342	0.0671	0.3718	-0.9999	-65.1725	-59.758
16	0.0664	-0.0991	0.0716	0.1121	-0.1179	0.1431	0.1248	0.0406	-0.008	-0.1675	-0.1322	-0.0655	0.2602	-0.0546	-0.0001	0.4608	-0.0822	0.0504	0.2868	0.0044	0.3035	0.1532	-71.1579	-46.948
17	0.134	0.0124	0.1333	0.0418	0.0457	0.135	0.14	0.0148	0.0906	-0.4019	-0.0572	0.0438	0.1568	-0.1193	-0.0018	0.5825	-0.0462	0.0911	0.2223	-0.0034	0.2486	3.6896	-73.5769	-52.4654
18	0.0438	0.0292	0.0655	0.0845	-0.0237	0.2702	-0.0431	-0.0291	-0.146	0.1836	0.01	0.0026	-0.3748	-0.1191	-0.0118	0.2497	0.0053	0.1119	0.2853	-0.0064	0.2914	-2.4093	-54.632	-18.7685
19	0.1639	-0.1144	0.1552	0.4035	-0.0998	0.1487	-0.0804	0.0421	-0.0175	0.1714	0.0805	-0.053	-0.2028	-0.0442	0	0.274	-0.0321	0.0456	0.2046	-0.0258	0.2453	5.3237	-61.5139	-15.5206
20	0.0495	0.05	0.027	0.2984	-0.0194	0.1059	-0.0332	-0.003	-0.0119	-0.1417	0.0444	0.0322	-0.1128	-0.1421	-0.0295	0.224	0.0048	0.0734	0.2866	0.0382	0.2744	-1.6848	-59.4647	-22.7354
21	0.1335	-0.0698	-0.0284	0.1899	-0.0408	0.1293	0.1032	-0.115	-0.0379	-0.1256	0.1669	-0.1239	0.1027	-0.2189	0.0191	0.3848	-0.1591	-0.0524	0.2995	0.0298	0.2879	-6.617	-62.3206	-53.3682
22	0.0293	-0.0828	0.0059	0.2194	-0.0116	0.0019	-0.064	0.0223	-0.0887	0.2186	0.1646	0.0349	-0.0404	-0.0773	0.0121	0.1856	-0.0274	0.0686	0.3141	0.0295	0.2569	-8.8921	-53.544	-45.7146
23	0.3983	0.0339	0.3575	0.3999	0.3878	0.6094	0.0509	0.0243	-0.1502	0.082	0.103	0.0678	0.2481	-0.221	0.0673	0.1893	-0.1328	0.0424	0.4404	0.0468	0.3112	-16.8055	-60.4738	-47.9888
24	0.33	-0.3736	-0.2857	0.4316	0.2949	0.2407	-0.216	0.057	-0.0503	-0.1105	0.2361	-0.0696	0.4611	-0.0255	-0.0437	0.3479	-0.2223	-0.0078	0.3131	-0.0101	0.2273	-7.3988	-61.7054	-47.7085
25	0.3237	-0.3425	-0.1208	0.5213	0.2089	0.1113	-0.0943	0.2988	0.2279	-0.2251	0.3621	0.0903	0.1348	-0.487	0.2158	0.3359	-0.1608	-0.1043	0.4739	0.058	0.2299	-12.645	-54.1789	-55.541

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 114 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 115 through 209 )	A
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 1 through 25 )	B
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 26 through 38 )	B
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 39 through 95B)	B
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 96 through 107 )	B
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 108 through 137 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 138 through 187 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 188 through 211 )	B
10	X-RAY DIFFRACTION	10	chain 'H' and (resid 2 through 17 )	H
11	X-RAY DIFFRACTION	11	chain 'H' and (resid 18 through 74 )	H
12	X-RAY DIFFRACTION	12	chain 'H' and (resid 75 through 87 )	H
13	X-RAY DIFFRACTION	13	chain 'H' and (resid 88 through 100E)	H
14	X-RAY DIFFRACTION	14	chain 'H' and (resid 101 through 119 )	H
15	X-RAY DIFFRACTION	15	chain 'H' and (resid 120 through 134 )	H
16	X-RAY DIFFRACTION	16	chain 'H' and (resid 135 through 175 )	H
17	X-RAY DIFFRACTION	17	chain 'H' and (resid 176 through 209 )	H
18	X-RAY DIFFRACTION	18	chain 'L' and (resid 1 through 25 )	L
19	X-RAY DIFFRACTION	19	chain 'L' and (resid 26 through 95B)	L
20	X-RAY DIFFRACTION	20	chain 'L' and (resid 96 through 107 )	L
21	X-RAY DIFFRACTION	21	chain 'L' and (resid 108 through 137 )	L
22	X-RAY DIFFRACTION	22	chain 'L' and (resid 138 through 149 )	L
23	X-RAY DIFFRACTION	23	chain 'L' and (resid 150 through 162 )	L
24	X-RAY DIFFRACTION	24	chain 'L' and (resid 163 through 187 )	L
25	X-RAY DIFFRACTION	25	chain 'L' and (resid 188 through 209 )	L

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Assembly

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Experiment

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About Yorodumi

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

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Yorodumi