PDB-6anp: CAT192 Fab Insertion Mutant H5/L0

ID or keywords:

Entry

Database: PDB / ID: 6anp

Title

CAT192 Fab Insertion Mutant H5/L0

Components

CAT192 Fab Heavy chain
CAT192 Fab Light chain

Keywords

IMMUNE SYSTEM / Fab / TGF-Beta / protein engineering / antibody engineering

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.45 Å

Authors

Lord, D.M. / Wei, R.R.

Citation

Journal: MAbs / Year: 2018
Title: Structure-based engineering to restore high affinity binding of an isoform-selective anti-TGF beta 1 antibody.
Authors: Lord, D.M. / Bird, J.J. / Honey, D.M. / Best, A. / Park, A. / Wei, R.R. / Qiu, H.

History

Deposition	Aug 14, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 31, 2018	Provider: repository / Type: Initial release
Revision 1.1	Feb 14, 2018	Group: Database references / Category: citation / Item: _citation.page_first / _citation.page_last
Revision 1.2	May 2, 2018	Group: Data collection / 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6anp.cif.gz	345.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6anp.ent.gz	283.2 KB	Display	PDB format
PDBx/mmJSON format	6anp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6anp_validation.pdf.gz	446.6 KB	Display	wwPDB validaton report
Full document	6anp_full_validation.pdf.gz	451.8 KB	Display
Data in XML	6anp_validation.xml.gz	36.4 KB	Display
Data in CIF	6anp_validation.cif.gz	52.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/an/6anp ftp://data.pdbj.org/pub/pdb/validation_reports/an/6anp	HTTPS FTP

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Related structure data

Related structure data	6amjSC 6ammC 6ao0C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6y1m-d 4qhk-1 7lka-3 3qg7-d 6h0e-2 4r7n-10 5cp7-3 1fh5-d 4r7n-7 4odu-1 5cd3-2 4trp-d 3giz-d 4ktd-d 5kg9-2 5mu0-8 4r7n-6 2o5z-d 4qhk-2 4yo0-1 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

6amjSC

6ammC

6ao0C

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

L: CAT192 Fab Light chain

A: CAT192 Fab Light chain

B: CAT192 Fab Heavy chain

H: CAT192 Fab Heavy chain

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

1

L: CAT192 Fab Light chain

H: CAT192 Fab Heavy chain

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

2

A: CAT192 Fab Light chain

B: CAT192 Fab Heavy chain

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

Unit cell

Length a, b, c (Å)	54.440, 83.890, 112.250
Angle α, β, γ (deg.)	90.000, 97.490, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Antibody	CAT192 Fab Light chain Mass: 23167.650 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody	CAT192 Fab Heavy chain Mass: 24907.574 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 538 / 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: 2.64 Å³/Da / Density % sol: 53.46 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 10.3% PEG 20K, 0.0938M MES pH 6.0, 2.5% DMSO

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5419 Å
Detector	Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 21, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5419 Å / Relative weight: 1
Reflection	Resolution: 2.45→33.928 Å / Num. obs: 36532 / B_iso Wilson estimate: 29.84 Å²
Reflection shell	Resolution: 2.45→2.58 Å / Redundancy: 3 % / R_merge(I) obs: 0.443 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5019 / % possible all: 93.7

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Processing

Software

Name	Version	Classification
PHENIX	1.12_2829	refinement
CrystalClear		data collection
SCALA		data scaling
PDB_EXTRACT	3.22	data extraction
iMOSFLM		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6AMJ

6amj

Resolution: 2.45→33.928 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.89 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2354	1806	4.94 %
R_work	0.1831	34726	-
obs	0.1857	36532	98.79 %

Solvent computation

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

Displacement parameters

B_iso max: 142.64 Å² / B_iso mean: 37.8094 Å² / B_iso min: 12.21 Å²

Refinement step

Cycle: final / Resolution: 2.45→33.928 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6408	0	0	538	6946
B_iso mean	-	-	-	38.35	-
Num. residues	-	-	-	-	852

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	6557
X-RAY DIFFRACTION	f_angle_d	0.564	8922
X-RAY DIFFRACTION	f_chiral_restr	0.043	1014
X-RAY DIFFRACTION	f_plane_restr	0.004	1139
X-RAY DIFFRACTION	f_dihedral_angle_d	9.032	3872

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 13

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.45-2.5163	0.3256	116	0.2477	2406	2522	89
2.5163-2.5903	0.2644	132	0.2378	2666	2798	98
2.5903-2.6738	0.2992	146	0.2353	2632	2778	99
2.6738-2.7694	0.3152	106	0.2203	2700	2806	99
2.7694-2.8802	0.2689	150	0.2232	2695	2845	99
2.8802-3.0112	0.269	145	0.2133	2662	2807	100
3.0112-3.1699	0.2574	139	0.2092	2675	2814	100
3.1699-3.3683	0.3039	128	0.1987	2719	2847	100
3.3683-3.6281	0.2402	143	0.1713	2709	2852	100
3.6281-3.9927	0.2379	149	0.1716	2680	2829	100
3.9927-4.5692	0.1809	145	0.14	2712	2857	100
4.5692-5.7522	0.1549	127	0.139	2716	2843	100
5.7522-33.9313	0.2074	180	0.1701	2754	2934	100

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	0.3365	0.4999	0.7308	1.4954	0.768	3.7492	-0.0347	0.0363	-0.0062	-0.3566	0.0738	-0.0131	-0.0005	0.2235	-0.0905	0.3094	0.0431	0.0242	0.2556	0.0423	0.2478	178.3326	-9.5384	129.4268
2	2.9708	-0.2952	1.983	1.1994	-0.845	4.3144	-0.1493	0.0225	0.4075	-0.3241	0.0396	-0.2374	-0.4273	0.3011	0.0815	0.2764	-0.043	0.043	0.2117	0.0296	0.3133	180.5796	-3.3596	131.2366
3	1.6947	2.4176	-2.3707	3.3073	-3.4148	3.4224	-0.0141	-0.4509	-0.1543	-0.2016	-0.29	-0.3947	0.0362	0.6186	0.2111	0.1822	0.0008	0.0417	0.3036	-0.0179	0.2691	174.3987	-15.6433	149.5326
4	8.5409	-3.1762	4.1578	4.2219	-2.3635	4.0572	0.0457	-0.2204	0.539	0.1359	-0.1661	0.3046	0.2239	-0.3349	0.1813	0.2041	-0.0114	-0.0007	0.2468	-0.1223	0.2632	145.3364	-12.9125	156.9449
5	9.0445	0.2579	0.6115	1.114	-1.086	1.9467	-0.0622	-0.2026	-0.1709	-0.1781	0.0343	-0.2111	0.1735	0.1153	0.044	0.1838	0.0246	-0.0033	0.1648	-0.0404	0.1487	157.946	-18.5919	150.3813
6	4.3822	1.73	-0.0914	3.7153	-1.0091	0.833	0.0324	0.5762	-0.1831	0.145	0.1412	-0.1909	0.2885	0.1626	-0.1503	0.2651	-0.0178	-0.0052	0.2498	-0.0733	0.1524	150.3868	-20.6248	145.3447
7	7.6004	2.9919	-1.0685	2.4608	-2.5965	7.7421	0.2631	-0.4982	1.2772	0.2555	0.3581	0.6551	-0.3104	0.4752	-0.5906	0.2602	0.0534	0.0165	0.269	-0.1057	0.335	170.3384	-9.2304	152.297
8	3.2199	-1.106	0.4106	3.5005	-0.5598	1.2187	0.03	0.2895	-0.31	-0.104	0.0908	0.4421	0.0518	-0.1976	-0.1285	0.1784	-0.0089	0.0002	0.2152	-0.0123	0.2124	145.3736	-20.3799	150.9067
9	4.3156	0.7202	1.275	3.9412	-0.3514	1.0494	0.4432	-1.152	-0.8525	0.0977	-0.1885	-0.0892	-0.2117	-0.0033	-0.0711	0.2549	-0.0258	0.048	0.1851	0.0525	0.2577	154.3581	-25.1423	157.2443
10	4.7461	-0.9722	-2.8177	0.7719	0.7365	1.8736	0.1465	-0.4962	0.3572	-0.0374	-0.0501	-0.1173	0.0071	0.2818	0.0005	0.1961	-0.023	0.0186	0.2332	0.0133	0.1941	157.0332	-37.5192	155.64
11	5.5	-0.559	-0.9987	2.7953	0.5386	1.9217	0.0239	-0.5157	-0.5756	0.311	-0.1074	0.2183	0.1842	0.273	0.1307	0.2349	-0.0537	-0.0397	0.3058	0.0975	0.314	151.1318	-46.4036	158.1093
12	5.5628	-0.6213	1.1664	4.2715	-0.5026	0.5354	0.4401	-1.3417	-0.1431	1.1271	-0.6842	-0.3132	0.1624	0.2355	-0.0932	0.3345	-0.0721	-0.0574	0.4768	0.1462	0.165	153.702	-41.7176	164.1977
13	5.2523	0.1365	-0.5393	1.0944	-0.0268	1.4213	0.1495	-0.3946	-0.3331	0.0722	-0.177	0.0713	0.0917	0.0887	0.0222	0.208	0.0064	0.0039	0.2635	0.0235	0.2151	151.5327	-43.9184	154.4997
14	2.9456	0.7305	-1.2606	3.0534	-0.2446	0.5671	-0.4519	-0.4594	-0.1459	0.1286	-0.0557	0.2011	0.3592	0.3721	0.3791	0.2709	0.0284	0.0236	0.4141	0.0877	0.2196	169.9649	-37.2818	145.5804
15	6.3054	0.3324	1.7027	3.4947	-0.0797	4.1342	0.0707	0.4807	-0.0809	-0.7168	0.2338	0.2475	0.5438	0.0321	-0.4312	0.464	-0.02	-0.0823	0.2715	-0.0193	0.2716	163.788	-29.8263	117.0435
16	2.3889	-1.2181	2.0283	2.8853	-3.5635	5.2681	-0.0435	-0.1806	-0.095	0.2273	0.2404	0.3528	-0.2898	-0.2976	-0.1498	0.2633	0.0369	0.0652	0.215	-0.0306	0.1974	165.4345	-28.1149	132.1778
17	0.7009	0.7459	-0.141	0.929	0.5879	1.7465	-0.3127	0.11	0.0701	-0.088	0.4534	-0.3724	0.1356	-0.1798	-0.1111	0.2314	0.0349	0.0349	0.2873	-0.0625	0.3062	159.2181	-21.9015	128.8115
18	6.5892	1.6468	4.2629	4.5168	-3.9843	9.3873	-0.0099	-0.0751	-0.2367	0.186	-0.0654	-0.0462	-0.0872	-0.0575	0.1105	0.3662	0.1041	-0.0499	0.1815	-0.0229	0.2333	167.8887	-41.7367	139.1403
19	4.5062	-0.1618	2.1754	3.2318	-2.3524	6.2235	-0.0897	0.4527	0.3177	-0.0958	0.1278	0.1109	-0.1651	-0.0065	-0.0827	0.2651	0.0127	0.0338	0.1826	-0.0053	0.2618	166.2074	-21.9888	124.1778
20	4.4062	0.1135	-1.3464	2.4874	0.122	3.8019	-0.5442	0.9004	-0.5376	-0.4366	0.6409	0.1281	0.8675	-0.7527	-0.2457	0.3887	-0.1421	-0.0248	0.4836	-0.0335	0.3428	135.9164	-54.3323	139.9258
21	4.917	0.5769	-1.8699	2.0645	-1.1837	4.6901	-0.041	0.794	0.1069	-0.11	0.2373	0.3281	0.1182	-0.6029	-0.1755	0.194	-0.0121	-0.0266	0.3632	0.0704	0.249	134.2747	-47.6764	144.7889
22	3.6222	1.3438	-3.6655	0.5574	-0.4936	7.7153	-0.1989	0.4415	0.0611	0.0144	0.3788	0.4096	-0.2022	-1.5187	-0.196	0.2568	-0.0299	-0.0137	0.4306	-0.0015	0.4046	142.2771	-48.5512	138.8097
23	4.1678	-0.0218	0.4446	1.3247	-0.4543	3.9314	0.0123	0.2805	-0.1094	-0.1871	0.1157	0.1267	0.3145	-0.0475	-0.0523	0.308	-0.0383	-0.038	0.1519	-0.0373	0.2231	161.5575	-39.5565	123.1245
24	3.9801	0.2966	0.5892	2.7822	-0.2579	2.5118	-0.0876	0.697	-0.1681	-0.3608	0.0877	0.1218	0.5486	0.1439	0.0273	0.3811	0.0057	-0.0271	0.253	-0.0781	0.2058	165.921	-43.1262	120.4115
25	2.8401	0.9779	-0.2167	4.4013	0.6536	5.0421	0.1082	1.5027	-0.0854	-1.179	0.0703	0.0247	-0.5323	0.0715	-0.1747	0.6136	-0.0453	-0.0647	0.5447	-0.0654	0.3464	163.9354	-42.1747	112.9857
26	3.22	1.6629	-0.2515	4.2216	-2.014	4.4389	-0.1487	0.0745	0.3429	0.2106	0.1018	-0.4229	-1.0005	-0.0454	0.0666	0.5732	0.0431	-0.1049	0.2284	0.0668	0.6437	164.2013	14.9824	127.9742
27	3.5512	-0.9142	-0.3646	2.2236	-1.1729	4.668	-0.2723	0.079	0.2111	-0.2849	0.1507	-0.0282	-0.2423	-0.205	0.0726	0.4131	0.0313	-0.0366	0.2364	0.0785	0.3568	163.4155	8.1362	122.7692
28	2.7082	0.2213	-1.3425	1.3145	-0.2001	1.9963	0.0207	0.3776	0.2609	0.1148	0.0864	0.2044	-0.2174	-0.4919	0.0316	0.22	0.0546	-0.0274	0.1823	-0.0367	0.3248	153.0767	-2.1275	148.1542
29	2.6298	-0.4689	0.3	1.3452	-0.6929	3.1181	-0.0011	-0.014	0.4359	0.1053	-0.0602	-0.2003	-0.1742	0.0026	0.0778	0.1804	0.023	0.0019	0.2053	-0.0592	0.2874	154.3612	-3.0132	156.1232
30	3.7786	-1.1396	0.9993	7.8026	-1.6299	4.9139	0.0859	-0.498	0.4876	0.7564	0.2311	0.4679	-0.8016	-0.6524	-0.2105	0.3019	0.0926	0.0392	0.4287	-0.1934	0.453	146.8587	-0.2618	161.6234

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'L' and (resid 1 through 38 )	L	1 - 38
2	X-RAY DIFFRACTION	2	chain 'L' and (resid 39 through 102 )	L	39 - 102
3	X-RAY DIFFRACTION	3	chain 'L' and (resid 103 through 113 )	L	103 - 113
4	X-RAY DIFFRACTION	4	chain 'L' and (resid 114 through 128 )	L	114 - 128
5	X-RAY DIFFRACTION	5	chain 'L' and (resid 129 through 150 )	L	129 - 150
6	X-RAY DIFFRACTION	6	chain 'L' and (resid 151 through 163 )	L	151 - 163
7	X-RAY DIFFRACTION	7	chain 'L' and (resid 164 through 174 )	L	164 - 174
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 175 through 197 )	L	175 - 197
9	X-RAY DIFFRACTION	9	chain 'L' and (resid 198 through 214 )	L	198 - 214
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 1 through 18 )	A	1 - 18
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 19 through 61 )	A	19 - 61
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 62 through 75 )	A	62 - 75
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 76 through 102 )	A	76 - 102
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 103 through 113 )	A	103 - 113
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 114 through 128 )	A	114 - 128
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 129 through 150 )	A	129 - 150
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 151 through 163 )	A	151 - 163
18	X-RAY DIFFRACTION	18	chain 'A' and (resid 164 through 174 )	A	164 - 174
19	X-RAY DIFFRACTION	19	chain 'A' and (resid 175 through 214 )	A	175 - 214
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 3 through 32 )	B	3 - 32
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 33 through 99 )	B	33 - 99
22	X-RAY DIFFRACTION	22	chain 'B' and (resid 100 through 134 )	B	100 - 134
23	X-RAY DIFFRACTION	23	chain 'B' and (resid 135 through 190 )	B	135 - 190
24	X-RAY DIFFRACTION	24	chain 'B' and (resid 191 through 218 )	B	191 - 218
25	X-RAY DIFFRACTION	25	chain 'B' and (resid 219 through 229 )	B	219 - 229
26	X-RAY DIFFRACTION	26	chain 'H' and (resid 3 through 33 )	H	3 - 33
27	X-RAY DIFFRACTION	27	chain 'H' and (resid 34 through 98 )	H	34 - 98
28	X-RAY DIFFRACTION	28	chain 'H' and (resid 99 through 149 )	H	99 - 149
29	X-RAY DIFFRACTION	29	chain 'H' and (resid 150 through 218 )	H	150 - 218
30	X-RAY DIFFRACTION	30	chain 'H' and (resid 219 through 229 )	H	219 - 229

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Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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-Related structure data

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-Experimental details

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-Sample preparation

-Data collection

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+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

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

+
Open data

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Basic information

-
Structure visualization

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Downloads & links

-
Download

-
Validation report

-
Related structure data

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Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

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Sample preparation

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Data collection

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Processing

+
About Yorodumi

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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

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Yorodumi