PDB-6ugt: Crystal structure of the Fab fragment of PF06438179/GP1111 an inf...

ID or keywords:

Entry

Database: PDB / ID: 6ugt

Title

Crystal structure of the Fab fragment of PF06438179/GP1111 an infliximab biosimilar in a I-centered orthorhombic crystal form, Lot A

Components

PF06438179 Fab Heavy Chain
PF06438179 Fab Light Chain

Keywords

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

Function / homology

Function and homology information

immunoglobulin complex / adaptive immune response / extracellular region / plasma membrane
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.15 Å

Authors

Lerch, T.F. / Sharpe, P. / Mayclin, S.J. / Edwards, T.E. / Polleck, S. / Rouse, J.C. / Conlan, H.D.

Citation

Journal: BioDrugs / Year: 2020
Title: Crystal Structures of PF-06438179/GP1111, an Infliximab Biosimilar.
Authors: Lerch, T.F. / Sharpe, P. / Mayclin, S.J. / Edwards, T.E. / Polleck, S. / Rouse, J.C. / Zou, Q. / Conlon, H.D.

History

Deposition	Sep 26, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 13, 2019	Provider: repository / Type: Initial release
Revision 1.1	Feb 12, 2020	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2	Oct 11, 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 1.3	Oct 9, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6ugt.cif.gz	357.4 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	6ugt_validation.pdf.gz	264.6 KB	Display	wwPDB validaton report
Full document	6ugt_full_validation.pdf.gz	264.6 KB	Display
Data in XML	6ugt_validation.xml.gz	1.4 KB	Display
Data in CIF	6ugt_validation.cif.gz	13.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ug/6ugt ftp://data.pdbj.org/pub/pdb/validation_reports/ug/6ugt	HTTPS FTP

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Related structure data

Related structure data	6ugsC 6uguC 6ugvC 6ugwC 6ugxC 6ugyC 4g3yS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4yhm-d 4ygv-1 6df2-2 6ugv-2 5w24-d 3utz-1 4yhn-2 6nv0-2 3o2w-d 6ugv-1 6nov-2 4hdi-2 4r7n-3 5k8a-1 5vh4-2 5t78-1 6w4w-d 4ygv-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 - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

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

H: PF06438179 Fab Heavy Chain

L: PF06438179 Fab Light Chain

A: PF06438179 Fab Heavy Chain

B: PF06438179 Fab Light Chain

hetero molecules

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

1

H: PF06438179 Fab Heavy Chain

L: PF06438179 Fab Light Chain

hetero molecules

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

2

A: PF06438179 Fab Heavy Chain

B: PF06438179 Fab Light Chain

hetero molecules

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

Unit cell

Length a, b, c (Å)	90.600, 93.330, 316.560
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	24
Space group name H-M	I2₁2₁2₁

Components on special symmetry positions

ID	Model	Components
1	1	H-474- HOH
2	1	H-486- HOH
3	1	A-552- HOH

#1: Antibody	PF06438179 Fab Heavy Chain Mass: 24356.178 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse) / References: UniProt: A8K008
#2: Antibody	PF06438179 Fab Light Chain Mass: 23460.873 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse) / References: UniProt: Q6P5S8
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 652 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 3.47 Å³/Da / Density % sol: 64.57 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 10 mg/mL PF06438179 Fab lot A against 2.16 M sodium malonate, 4% v/v t-butanol, crystal tracking ID 267662h2, unique puck ID sdw5-8

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

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

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Nov 19, 2015

Radiation

Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97856 Å / Relative weight: 1

Reflection

Resolution: 2.15→50 Å / Num. obs: 72719 / % possible obs: 99.1 % / Redundancy: 4.928 % / B_iso Wilson estimate: 26.74 Å² / CC_1/2: 0.994 / R_merge(I) obs: 0.108 / R_rim(I) all: 0.121 / Χ²: 0.956 / Net I/σ(I): 10.74

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
2.15-2.21	5.084	0.565	3.08	5315	0.788	0.633	98.7
2.21-2.27	5.079	0.482	3.58	5154	0.83	0.54	98.7
2.27-2.33	5.064	0.436	3.86	5027	0.862	0.489	98.9
2.33-2.4	5.064	0.383	4.35	4892	0.882	0.429	99
2.4-2.48	5.068	0.335	4.9	4764	0.911	0.376	98.9
2.48-2.57	5.035	0.283	5.72	4581	0.935	0.317	99.2
2.57-2.67	5.001	0.227	6.93	4487	0.957	0.255	99.2
2.67-2.78	4.989	0.181	8.4	4250	0.97	0.203	99.2
2.78-2.9	4.938	0.144	9.88	4134	0.982	0.162	99.3
2.9-3.04	4.882	0.118	11.93	3956	0.985	0.133	99.3
3.04-3.21	4.8	0.092	14.3	3753	0.991	0.103	99.4
3.21-3.4	4.768	0.078	16.49	3573	0.991	0.088	99.4
3.4-3.63	4.775	0.068	18.16	3367	0.992	0.077	99.3
3.63-3.93	4.711	0.061	19.51	3142	0.994	0.069	99.3
3.93-4.3	4.74	0.055	20.86	2887	0.995	0.062	99.4
4.3-4.81	4.748	0.051	22.46	2619	0.996	0.058	99.3
4.81-5.55	4.778	0.052	21.59	2344	0.995	0.058	99.3
5.55-6.8	4.846	0.05	20.45	2006	0.996	0.056	99.7
6.8-9.62	4.735	0.047	22	1575	0.996	0.053	99.4
9.62-50	4.392	0.047	23.13	893	0.991	0.053	95.1

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Processing

Software

Name	Version	Classification
PHENIX		refinement
XDS		data reduction
XSCALE		data scaling
PDB_EXTRACT	3.25	data extraction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 4G3Y

4g3y

Resolution: 2.15→50 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.88

	R_factor	Num. reflection	% reflection
R_free	0.2281	3533	4.86 %
R_work	0.1846	-	-
obs	0.1867	72699	99.09 %

Solvent computation

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

Displacement parameters

B_iso max: 98.52 Å² / B_iso mean: 33.3042 Å² / B_iso min: 11.21 Å²

Refinement step

Cycle: final / Resolution: 2.15→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6548	0	28	652	7228
B_iso mean	-	-	43.96	38.61	-
Num. residues	-	-	-	-	866

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	6771
X-RAY DIFFRACTION	f_angle_d	0.865	9220
X-RAY DIFFRACTION	f_chiral_restr	0.053	1031
X-RAY DIFFRACTION	f_plane_restr	0.005	1186
X-RAY DIFFRACTION	f_dihedral_angle_d	13.448	4019

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
2.15-2.1794	0.2948	145	0.2351	2718	99
2.1794-2.2105	0.3373	117	0.2305	2759	99
2.2105-2.2435	0.2782	142	0.2219	2722	99
2.2435-2.2786	0.2751	138	0.215	2733	99
2.2786-2.3159	0.2256	122	0.2145	2723	99
2.3159-2.3559	0.285	143	0.216	2721	99
2.3559-2.3987	0.2927	142	0.2279	2766	99
2.3987-2.4448	0.2692	119	0.2243	2739	99
2.4448-2.4947	0.2685	147	0.2205	2707	99
2.4947-2.549	0.2582	136	0.2078	2760	99
2.549-2.6083	0.2529	126	0.1967	2765	99
2.6083-2.6735	0.2203	150	0.1904	2769	99
2.6735-2.7458	0.2183	163	0.1965	2723	99
2.7458-2.8266	0.2462	156	0.2038	2731	99
2.8266-2.9178	0.2511	140	0.2048	2765	99
2.9178-3.022	0.2571	137	0.1973	2762	99
3.022-3.143	0.2319	126	0.1938	2785	99
3.143-3.286	0.2537	160	0.1896	2743	100
3.286-3.4592	0.225	153	0.186	2769	99
3.4592-3.6758	0.2119	132	0.1804	2780	99
3.6758-3.9594	0.227	155	0.1718	2801	99
3.9594-4.3575	0.1978	137	0.1468	2815	99
4.3575-4.9873	0.1637	148	0.1299	2805	99
4.9873-6.2805	0.1891	145	0.1525	2858	99
6.2805-50	0.1844	154	0.1764	2947	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	1.884	0.9039	1.3742	2.0611	0.879	3.1778	0.0063	0.1433	0.0225	-0.0194	-0.0229	-0.0806	0.0452	0.2209	0.0251	0.1163	0.0122	0.0035	0.2002	0.0175	0.1129	-10.8358	6.1387	11.0419
2	2.0125	-0.2899	1.403	1.5293	-0.838	1.416	-0.1043	-0.1679	-0.2269	0.468	0.0172	-0.2281	0.2786	0.5525	0.0916	0.4104	0.2081	0.0298	0.3915	0.0609	0.2901	5.6633	-1.0441	35.4723
3	0.9577	0.7415	-0.1326	5.7677	-0.6951	0.4179	-0.0974	0.0753	0.0416	-0.1234	-0.0362	-0.3353	0.1521	0.2151	0.1124	0.3007	0.1362	-0.0167	0.3864	0.0581	0.2337	5.9857	-6.7712	33.5916
4	3.4411	-2.922	2.4574	6.9924	-5.8168	8.0569	-0.1347	-0.1896	-0.3429	0.3756	0.2486	0.2076	-0.0471	-0.3177	-0.2094	0.1274	0.0038	0.0193	0.2257	0.0128	0.1658	-30.1121	-2.7386	26.2063
5	8.1139	-0.2007	2.9929	5.8817	-0.064	6.8827	0.4676	-0.0658	-0.6883	0.1229	-0.0975	-0.3776	0.6367	0.5804	-0.2146	0.1916	-0.0206	0.0015	0.1982	0.0154	0.1382	-18.9441	-6.6891	20.8089
6	3.0066	-1.9047	0.5971	5.5968	-1.0898	3.3536	-0.0432	0.1085	-0.4201	-0.1616	0.1785	0.2208	0.6342	-0.1199	-0.0942	0.2509	-0.1086	-0.0299	0.2165	-0.0141	0.225	-29.057	-10.6833	18.6595
7	1.1393	-0.6277	0.6427	0.7095	-1.0971	1.9679	-0.0575	-0.0769	-0.0853	-0.0258	0.09	-0.0608	0.2972	0.1128	-0.0673	0.2519	0.054	-0.007	0.1815	-0.0182	0.1764	-13.18	-6.1941	32.2698
8	4.0377	2.3908	0.9028	4.4006	1.3915	0.4825	-0.1337	-0.2748	0.2719	0.1684	0.0261	0.0192	-0.0529	0.01	0.0858	0.3081	0.1148	-0.03	0.2903	0.0506	0.2206	-4.3619	-5.4772	47.1319
9	4.2639	2.4405	0.6096	3.5675	-0.009	1.1353	-0.0988	-0.7136	0.0251	0.2367	-0.2169	-0.3931	-0.0319	0.273	0.2478	0.3734	0.1615	-0.0667	0.4615	0.0272	0.243	4.151	-5.4819	54.2011
10	2.2373	0.2552	-0.1952	1.9518	-1.0077	3.2632	-0.1154	-0.0583	0.1756	0.1703	0.0419	-0.0792	-0.1473	-0.0787	0.0642	0.1632	0.0082	-0.0194	0.0907	-0.0056	0.1573	-16.1675	11.6164	68.0945
11	3.0732	-1.3068	0.6454	2.6802	-2.0036	3.1206	-0.0182	0.2833	0.5019	-0.2666	-0.2519	0.0113	-0.3652	-0.2915	0.2596	0.3091	0.0832	-0.0879	0.2761	0.0168	0.3403	-22.8476	28.1174	43.4057
12	6.0519	-1.3294	1.0338	2.0517	-1.1054	0.9481	-0.2776	-0.2832	0.5828	0.3772	0.0756	-0.2746	-0.2924	-0.1995	0.2009	0.295	0.1224	-0.0979	0.3226	-0.0661	0.2923	-28.4768	28.7224	45.3397
13	6.3188	-1.8892	4.3102	1.7515	-1.6465	5.4446	0.1223	0.4834	-0.1529	-0.2747	-0.0425	0.2444	0.3046	0.1731	-0.1665	0.3036	0.0043	-0.0153	0.1591	-0.0128	0.2066	-25.3743	-7.4135	53.0347
14	5.2362	0.71	-0.4548	6.6057	-4.9536	6.8402	0.2245	0.1995	0.325	0.2861	-0.1617	0.4064	-0.7182	-0.3988	-0.0937	0.2461	-0.0109	-0.0203	0.1404	0.0118	0.1643	-29.1189	3.7697	58.5246
15	1.6324	-1.287	1.9514	3.9713	-2.5805	3.1019	0.1963	-0.2198	-0.2191	0.0738	0.1078	0.515	0.1431	-0.6796	-0.2747	0.2436	-0.1091	0.0143	0.2306	0.0205	0.2695	-33.2741	-6.2352	60.6316
16	4.6418	-0.9166	2.4632	1.8684	-1.0772	4.0617	-0.0348	0.1493	-0.094	0.0384	0.2634	0.5336	-0.0386	-0.3617	-0.2323	0.1762	-0.0588	0.0042	0.2067	0.0384	0.2375	-32.3585	0.8755	53.0772
17	0.4813	-0.6722	0.8968	1.0445	-0.9581	2.1572	0.0511	0.0475	0.1446	-0.1016	-0.1873	-0.0761	-0.0215	-0.0217	0.1134	0.1879	0.0368	0.0147	0.2223	0.0289	0.2353	-27.3668	15.7292	38.7339
18	5.6694	2.9974	-2.7145	3.5803	-1.8753	2.6209	0.1853	0.0835	0.0024	0.2056	-0.0661	-0.197	-0.3637	-0.129	-0.0297	0.2154	0.0787	-0.0296	0.2242	0.0068	0.2294	-27.1863	17.0942	33.6313
19	2.9	1.4052	1.0256	3.7708	-0.1468	2.0718	-0.2648	0.6289	0.4673	-0.3719	0.0476	-0.0983	-0.3031	0.1538	0.231	0.3211	0.0984	0.0027	0.3018	0.0954	0.2727	-27.1781	26.4553	24.7871

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 113 )	H	1 - 113
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 114 through 141 )	H	114 - 141
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 142 through 220 )	H	142 - 220
4	X-RAY DIFFRACTION	4	chain 'L' and (resid 1 through 32 )	L	1 - 32
5	X-RAY DIFFRACTION	5	chain 'L' and (resid 33 through 48 )	L	33 - 48
6	X-RAY DIFFRACTION	6	chain 'L' and (resid 49 through 75 )	L	49 - 75
7	X-RAY DIFFRACTION	7	chain 'L' and (resid 76 through 128 )	L	76 - 128
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 129 through 174 )	L	129 - 174
9	X-RAY DIFFRACTION	9	chain 'L' and (resid 175 through 213 )	L	175 - 213
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 1 through 113 )	A	1 - 113
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 114 through 141 )	A	114 - 141
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 142 through 220 )	A	142 - 220
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 1 through 32 )	B	1 - 32
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 33 through 48 )	B	33 - 48
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 49 through 75 )	B	49 - 75
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 76 through 90 )	B	76 - 90
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 91 through 150 )	B	91 - 150
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 151 through 174 )	B	151 - 174
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 175 through 213 )	B	175 - 213

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-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi