PDB-5vh3: Crystal structure of Fab fragment of the anti-TNFa antibody infli...

ID or keywords:

Entry

Database: PDB / ID: 5vh3

Title

Crystal structure of Fab fragment of the anti-TNFa antibody infliximab in a C-centered orthorhombic crystal form

Components

Infliximab Fab Heavy Chain
Infliximab Fab Light Chain

Keywords

IMMUNE SYSTEM / antibody / Fab / infliximab / biosimilar / TNFa

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta

Function and homology information

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2 Å

Authors

Mayclin, S.J. / Edwards, T.E. / Lerch, T.F. / Conlan, H. / Sharpe, P.

Citation

Journal: MAbs / Year: 2017
Title: Infliximab crystal structures reveal insights into self-association.
Authors: Lerch, T.F. / Sharpe, P. / Mayclin, S.J. / Edwards, T.E. / Lee, E. / Conlon, H.D. / Polleck, S. / Rouse, J.C. / Luo, Y. / Zou, Q.

History

Deposition	Apr 12, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 3, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jun 7, 2017	Group: Database references
Revision 1.2	Aug 2, 2017	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Oct 4, 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 1.4	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5vh3.cif.gz	362.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5vh3.ent.gz	294.5 KB	Display	PDB format
PDBx/mmJSON format	5vh3.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/vh/5vh3 ftp://data.pdbj.org/pub/pdb/validation_reports/vh/5vh3	HTTPS FTP

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Related structure data

Related structure data	5vh4C 5vh5C 4g3yS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6xli-1 5t0y-1 6al4-3 6p9i-1 5mu0-1 2fjf-6 6wos-d 1rih-d 1wcb-2 4why-1 6ugu-1 1kcr-d 6c5i-d 7k8p-d 5t0y-3 4xbg-1 6ws6-3 6co3-d 4xxd-1 5ywf-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 - HomologyF&H Search

Related structure data

5vh4C

5vh5C

4g3yS

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

H: Infliximab Fab Heavy Chain

L: Infliximab Fab Light Chain

A: Infliximab Fab Heavy Chain

B: Infliximab Fab Light Chain

hetero molecules

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

1

H: Infliximab Fab Heavy Chain

L: Infliximab Fab Light Chain

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

2

A: Infliximab Fab Heavy Chain

B: Infliximab Fab Light Chain

hetero molecules

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

Unit cell

Length a, b, c (Å)	86.580, 138.820, 195.460
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

#1: Antibody	Infliximab Fab Heavy Chain Mass: 24356.178 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody	Infliximab Fab Light Chain Mass: 23460.873 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1046 / Source method: isolated from a natural source / Formula: H₂O
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: 3.07 Å³/Da / Density % sol: 59.94 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Fab at 10 mg/mL against Wiz 34 screen condition B4 20% PEG 3350, 0.2 M potassium citrate tribasic supplemented with 20% ethylene glycol as cryo-protectant, crystal tracking ID 267664b4, unique puck ID sdw5-2

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-G / Wavelength: 0.97856 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 19, 2015

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97856 Å / Relative weight: 1

Reflection

Resolution: 2→50 Å / Num. obs: 79590 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.246 % / B_iso Wilson estimate: 21.24 Å² / CC_1/2: 0.994 / R_merge(I) obs: 0.126 / R_rim(I) all: 0.137 / Χ²: 0.964 / Net I/σ(I): 10.52

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2-2.05	6.289	0.539	3.7	5830	0.889	0.588	100
2.05-2.11	6.291	0.458	4.29	5702	0.908	0.5	100
2.11-2.17	6.297	0.38	5.01	5521	0.939	0.414	100
2.17-2.24	6.308	0.324	5.82	5361	0.949	0.353	100
2.24-2.31	6.296	0.287	6.41	5220	0.959	0.313	100
2.31-2.39	6.311	0.266	6.85	5049	0.963	0.29	100
2.39-2.48	6.286	0.225	7.76	4880	0.973	0.246	100
2.48-2.58	6.292	0.195	8.81	4688	0.978	0.212	100
2.58-2.7	6.283	0.165	10.14	4498	0.984	0.18	100
2.7-2.83	6.265	0.144	11.27	4343	0.987	0.157	100
2.83-2.98	6.265	0.124	12.91	4081	0.989	0.135	100
2.98-3.16	6.232	0.107	14.7	3905	0.991	0.116	100
3.16-3.38	6.214	0.094	16.36	3645	0.991	0.103	99.9
3.38-3.65	6.165	0.085	17.73	3444	0.993	0.093	99.9
3.65-4	6.183	0.082	18.66	3156	0.992	0.09	99.9
4-4.47	6.181	0.078	19.46	2866	0.992	0.085	100
4.47-5.16	6.162	0.075	20.13	2549	0.993	0.082	100
5.16-6.32	6.102	0.075	19.25	2182	0.993	0.082	100
6.32-8.94	6.001	0.072	19.37	1699	0.992	0.079	99.9
8.94-50	5.554	0.066	19.81	971	0.992	0.073	97.9

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
Coot		model building
PHENIX	dev_2229	refinement
PDB_EXTRACT	3.22	data extraction
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4g3y

4g3y

Resolution: 2→50 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.6

	R_factor	Num. reflection	% reflection
R_free	0.1996	3868	4.86 %
R_work	0.1597	-	-
obs	0.1617	79576	99.95 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 91.11 Å² / B_iso mean: 27.218 Å² / B_iso min: 4.1 Å²

Refinement step

Cycle: final / Resolution: 2→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6515	0	4	1047	7566
B_iso mean	-	-	46.02	36.27	-
Num. residues	-	-	-	-	864

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	6696
X-RAY DIFFRACTION	f_angle_d	0.788	9130
X-RAY DIFFRACTION	f_chiral_restr	0.053	1028
X-RAY DIFFRACTION	f_plane_restr	0.005	1171
X-RAY DIFFRACTION	f_dihedral_angle_d	13.08	3975

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / 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 (%)
2-2.0244	0.2778	122	0.2246	2667	2789	100
2.0244-2.05	0.2572	134	0.1968	2711	2845	100
2.05-2.077	0.2593	146	0.1892	2646	2792	100
2.077-2.1054	0.2607	143	0.1885	2712	2855	100
2.1054-2.1355	0.2294	116	0.185	2650	2766	100
2.1355-2.1674	0.2063	138	0.1723	2699	2837	100
2.1674-2.2013	0.2168	133	0.1658	2686	2819	100
2.2013-2.2373	0.2119	119	0.1704	2688	2807	100
2.2373-2.2759	0.1993	131	0.1727	2727	2858	100
2.2759-2.3173	0.2073	131	0.1691	2625	2756	100
2.3173-2.3619	0.2297	141	0.169	2699	2840	100
2.3619-2.4101	0.2076	119	0.174	2738	2857	100
2.4101-2.4625	0.2218	137	0.1705	2665	2802	100
2.4625-2.5198	0.2036	125	0.1734	2688	2813	100
2.5198-2.5828	0.2209	147	0.1658	2697	2844	100
2.5828-2.6526	0.2036	152	0.1661	2669	2821	100
2.6526-2.7306	0.2175	152	0.17	2695	2847	100
2.7306-2.8188	0.245	150	0.1669	2688	2838	100
2.8188-2.9195	0.187	125	0.1659	2724	2849	100
2.9195-3.0364	0.2101	134	0.1719	2707	2841	100
3.0364-3.1745	0.2198	125	0.168	2706	2831	100
3.1745-3.3419	0.1887	141	0.1584	2713	2854	100
3.3419-3.5512	0.1668	147	0.1543	2707	2854	100
3.5512-3.8253	0.1885	160	0.1484	2683	2843	100
3.8253-4.21	0.1842	154	0.1319	2732	2886	100
4.21-4.8187	0.1432	160	0.1132	2755	2915	100
4.8187-6.0691	0.1693	122	0.1345	2778	2900	100
6.0691-47.5173	0.2062	164	0.1728	2853	3017	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	1.5785	-0.1369	-0.2573	2.0733	1.28	2.4326	-0.0386	-0.0511	0.1003	-0.0708	0.0021	0.2479	-0.0835	-0.2338	-0.0241	0.1134	0.0574	-0.0252	0.1566	0.028	0.18	-32.4482	-16.4811	14.699
2	0.4009	-0.3316	0.2447	2.5093	0.5502	0.5365	-0.0184	-0.0164	0.0417	-0.0513	0.0324	0.2601	0.0006	-0.0842	0.0389	0.1288	0.0515	0.0142	0.1716	0.0413	0.1692	-29.9301	-21.8764	20.2868
3	2.5292	0.6045	-1.2431	2.555	-0.1175	4.4069	0.0902	0.0795	-0.1837	0.1357	-0.0513	0.0276	0.1989	-0.3706	-0.0469	0.149	0.0217	-0.0428	0.1635	-0.0037	0.1855	-21.4325	-51.6743	25.9508
4	3.9707	-1.1014	1.7962	3.1703	0.7287	1.3094	-0.0408	-0.2109	-0.282	0.6496	-0.2042	-0.0269	0.062	-0.0428	0.0612	0.2426	0.0843	0.0106	0.1831	-0.0168	0.1688	-12.9422	-18.9282	35.3305
5	1.5798	0.2167	0.1504	3.2464	-0.8359	1.7656	-0.1231	-0.3871	0.0388	0.5346	0.1455	0.0923	-0.0504	-0.0788	-0.0129	0.2417	0.1328	-0.0028	0.2619	-0.012	0.1436	-20.9121	-11.6655	35.5441
6	1.2202	0.0018	-0.0739	2.3056	-1.2301	3.1882	-0.2887	-0.3572	-0.0025	0.519	0.2878	0.0474	0.027	-0.0904	-0.0303	0.2223	0.1296	0.0134	0.2457	0.0218	0.1505	-20.7743	-15.5358	31.9969
7	4.353	-4.5316	1.5718	6.3437	-2.5264	3.1311	-0.0347	0.2324	0.2176	-0.0709	-0.1371	-0.1617	-0.4616	-0.0178	0.174	0.1838	0.012	-0.0293	0.1131	-0.0096	0.1205	-11.4791	-33.5106	41.9641
8	2.9774	0.3522	1.0934	3.226	1.947	7.3024	0.3114	0.3174	-0.5549	-0.222	-0.1535	0.2483	0.4364	-0.3889	-0.1105	0.2461	0.0569	-0.0731	0.1535	-0.0507	0.2882	-10.723	-55.7103	22.1121
9	1.4821	-2.27	-2.9335	4.5867	5.2801	6.9331	0.2013	0.0091	0.1041	-0.335	-0.0665	-0.108	-0.2975	0.0292	-0.0912	0.1739	0.0455	-0.0188	0.12	0.0126	0.1241	-6.2644	-43.479	29.3926
10	4.4658	-3.5396	-2.795	2.8466	2.2691	1.7776	0.4411	0.3768	0.5443	-0.1323	-0.2896	-0.2392	-0.2237	-0.2168	-0.2229	0.2811	0.0644	0.0054	0.1787	0.0374	0.2219	-2.2966	-43.615	20.8572
11	6.6433	0.3451	-3.5061	4.1006	3.2363	4.7303	0.0514	0.089	0.0177	-0.0961	-0.1327	0.0636	-0.2813	-0.6782	0.047	0.1994	0.0279	-0.0189	0.1801	-0.0182	0.1573	-17.1902	-37.7871	38.3941
12	3.2954	-2.1475	-1.4038	4.1587	3.6747	5.3585	0.22	0.1708	-0.1636	-0.1404	0.0469	-0.1345	0.17	0.1922	-0.2679	0.1667	0.0341	0.0017	0.1292	0.0152	0.182	-1.7446	-51.1867	24.6613
13	0.9916	-0.2359	0.3676	1.9946	-1.1668	2.5468	-0.0339	0.0008	-0.0458	-0.0463	0.0306	-0.2934	0.087	0.2777	0.0028	0.1132	0.0485	-0.0035	0.1778	-0.0505	0.182	29.7259	-52.5705	15.2264
14	1.2222	-1.0176	0.0796	4.1112	1.1483	3.1137	-0.0339	-0.0172	0.273	0.0835	0.0907	-0.2994	-0.3907	0.1837	-0.0546	0.1425	-0.0045	-0.0129	0.1769	-0.0216	0.2249	19.7278	-17.9703	21.6193
15	1.3865	-0.5284	-0.3294	2.2211	0.3585	0.853	-0.1773	-0.2407	0.0171	0.515	0.1795	-0.0883	0.0439	0.1693	0.0287	0.2652	0.1358	-0.037	0.2552	-0.0144	0.1627	17.7554	-54.2873	35.0212
16	0.484	-1.2347	-1.0102	2.7926	1.9338	0.9417	-0.1885	-0.1212	0.0592	0.403	0.2903	-0.1104	0.2071	0.3158	-0.1021	0.2199	0.091	-0.0368	0.2164	-0.0353	0.1863	16.8882	-47.1536	34.0548
17	3.83	-0.1661	-1.3361	5.1689	-2.3294	6.8221	0.3502	0.3818	0.6126	-0.0298	-0.1013	-0.3099	-0.9305	0.0481	-0.1215	0.2023	0.0556	0.0391	0.1339	0.0431	0.2712	8.2305	-12.5649	20.2359
18	2.1973	-2.4402	3.4836	4.8125	-5.4711	6.9312	0.1293	0.0227	-0.108	-0.1588	-0.0563	0.0302	0.1215	0.064	-0.0577	0.142	0.0484	-0.0016	0.1022	-0.041	0.1138	4.5581	-24.2408	28.7027
19	2.627	-2.1462	0.5706	2.0936	-1.1694	2.0129	0.0929	0.2808	-0.0689	-0.0865	-0.1753	0.09	0.0177	0.4015	0.0298	0.1386	0.0158	-0.0009	0.0966	-0.009	0.1687	7.664	-26.9102	28.3765
20	2.8598	-2.1377	1.5275	4.6285	-4.5953	6.9734	0.148	0.1729	0.0688	0.0098	0.1545	0.1575	-0.1726	-0.3652	-0.3159	0.1091	0.0198	-0.0363	0.1389	-0.015	0.1832	-0.3945	-16.9147	23.9487

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'H' and (resid 1 through 93 )	H	1 - 93
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 94 through 126 )	H	94 - 126
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 127 through 222 )	H	127 - 222
4	X-RAY DIFFRACTION	4	chain 'L' and (resid 1 through 18 )	L	1 - 18
5	X-RAY DIFFRACTION	5	chain 'L' and (resid 19 through 75 )	L	19 - 75
6	X-RAY DIFFRACTION	6	chain 'L' and (resid 76 through 102 )	L	76 - 102
7	X-RAY DIFFRACTION	7	chain 'L' and (resid 103 through 113 )	L	103 - 113
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 114 through 128 )	L	114 - 128
9	X-RAY DIFFRACTION	9	chain 'L' and (resid 129 through 150 )	L	129 - 150
10	X-RAY DIFFRACTION	10	chain 'L' and (resid 151 through 163 )	L	151 - 163
11	X-RAY DIFFRACTION	11	chain 'L' and (resid 164 through 174 )	L	164 - 174
12	X-RAY DIFFRACTION	12	chain 'L' and (resid 175 through 214 )	L	175 - 214
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 1 through 113 )	A	1 - 113
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 114 through 222 )	A	114 - 222
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 1 through 75 )	B	1 - 75
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 76 through 113 )	B	76 - 113
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 114 through 128 )	B	114 - 128
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 129 through 150 )	B	129 - 150
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 151 through 174 )	B	151 - 174
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 175 through 214 )	B	175 - 214

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Movie

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Open data

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Links

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Assembly

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Yorodumi