PDB-6amm: CAT192 Fab Insertion Mutant H0/L1

ID or keywords:

Entry

Database: PDB / ID: 6amm

Title

CAT192 Fab Insertion Mutant H0/L1

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: 2.8 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 10, 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	Mar 7, 2018	Group: Source and taxonomy / Category: entity_src_gen Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.3	May 2, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4	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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PDBx/mmCIF format	6amm.cif.gz	176.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6amm.ent.gz	141 KB	Display	PDB format
PDBx/mmJSON format	6amm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6amm_validation.pdf.gz	438 KB	Display	wwPDB validaton report
Full document	6amm_full_validation.pdf.gz	448 KB	Display
Data in XML	6amm_validation.xml.gz	17.3 KB	Display
Data in CIF	6amm_validation.cif.gz	22.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/am/6amm ftp://data.pdbj.org/pub/pdb/validation_reports/am/6amm	HTTPS FTP

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Related structure data

Related structure data	6amjSC 6anpC 6ao0C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3drt-d 6amj-2 2v7n-3 7lk9-1 3eo0-1 6o26-d 3f12-1 1rzi-2 4yny-1 5iie-1 6wk4-d 6dwi-4 4xcy-3 6ug7-d 6amj-1 6u6m-d 5ysl-1 6dwi-2 5bvj-4 5ds8-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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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

H: CAT192 Fab Heavy chain

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	72.790, 65.720, 110.448
Angle α, β, γ (deg.)	90.000, 102.830, 90.000
Int Tables number	5
Space group name H-M	I121

#1: Antibody	CAT192 Fab Light chain Mass: 23224.705 Da / Num. of mol.: 1 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: 24592.289 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.69 Å³/Da / Density % sol: 54.33 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 20% PEG 8K, 0.1M Sodium cacodylate pH 6.5, 0.2M MgCl2

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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 14, 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: 2.8→35.35 Å / Num. obs: 12663 / B_iso Wilson estimate: 40.07 Å²
Reflection shell	Resolution: 2.8→2.95 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.497 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1837 / % possible all: 100

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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: 2.8→35.35 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.97 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.3025	1266	10 %
R_work	0.2467	11397	-
obs	0.2522	12663	99.96 %

Solvent computation

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

Displacement parameters

B_iso max: 155.51 Å² / B_iso mean: 60.7622 Å² / B_iso min: 8.67 Å²

Refinement step

Cycle: final / Resolution: 2.8→35.35 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3209	0	0	0	3209
Num. residues	-	-	-	-	425

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	3284
X-RAY DIFFRACTION	f_angle_d	0.809	4469
X-RAY DIFFRACTION	f_chiral_restr	0.047	508
X-RAY DIFFRACTION	f_plane_restr	0.005	570
X-RAY DIFFRACTION	f_dihedral_angle_d	9.662	1941

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all
2.8-2.9121	0.3913	139	0.3145	1258	1397
2.9121-3.0445	0.3259	139	0.2873	1241	1380
3.0445-3.2049	0.3339	141	0.2705	1266	1407
3.2049-3.4056	0.3152	138	0.2585	1255	1393
3.4056-3.6683	0.3148	141	0.2651	1267	1408
3.6683-4.037	0.3633	140	0.2773	1249	1389
4.037-4.62	0.2681	141	0.2176	1280	1421
4.62-5.8165	0.2557	142	0.2062	1275	1417
5.8165-35.3527	0.2562	145	0.2158	1306	1451

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	1.3716	-1.643	-0.2374	1.9641	0.2847	0.0399	0.0201	-0.6987	0.2778	0.124	0.4196	-1.4473	-0.1033	1.1375	-0.2845	0.588	0.2004	0.0052	1.5701	-0.0503	0.981	-12.3078	-12.0179	-34.537
2	1.8715	-0.3217	-0.0301	2.1398	0.4528	0.9774	0.1207	0.2258	0.1835	-0.0174	-0.2444	-0.3104	-0.0107	0.1621	-0.0285	0.205	0.0937	-0.0198	-0.1093	0.0144	0.1514	-41.0796	2.3192	-28.5822
3	1.7372	0.4857	0.4048	3.9139	1.4456	1.4089	-0.2957	-0.1592	0.0858	0.4895	-0.1161	-0.1027	-0.0334	0.032	-0.1829	0.183	-0.1358	-0.1866	-0.2602	-0.1004	0.2347	-38.1401	0.2309	-24.0645
4	0.8601	0.1057	-0.3	1.262	-0.0769	1.7894	-0.0592	0.0469	0.5088	0.0052	-0.0018	0.2347	-0.5324	0.0604	-0.1673	0.2933	-0.013	-0.0814	-0.3035	0.1126	0.3197	-41.7237	11.7443	-25.4571
5	1.4115	0.8024	-0.7032	0.8515	-0.1582	0.5083	0.2845	-0.1154	-0.6295	0.0571	-0.5436	-0.2378	1.4222	1.0583	-0.0198	1.0105	0.4248	-0.1462	0.946	0.0281	0.6431	-19.1344	-20.2272	-14.8342
6	0.5185	0.6771	-0.5075	0.8911	-0.6652	0.4919	0.0119	-0.1389	-0.4447	-0.2835	-0.3117	-0.4324	1.0052	1.0042	-0.4953	1.1717	0.7261	-0.2885	1.4011	-0.0741	0.7378	-12.8032	-23.8069	-21.0617
7	1.2415	0.1406	0.2756	2.8072	-0.4269	0.1367	0.0408	0.217	-0.4826	-0.0393	0.0856	-1.1437	0.4572	1.1727	-0.2623	0.6626	0.3233	-0.1058	1.5599	-0.0475	0.6824	-8.0382	-12.7497	-21.3837
8	4.029	0.07	1.5169	3.849	-0.4449	1.513	0.2415	-0.5415	-0.5462	0.246	-0.125	-0.6589	0.5357	0.5514	-0.4883	0.835	0.622	-0.0717	1.1861	0.1462	0.8405	-12.3751	-17.3768	-15.9162
9	3.1183	-0.0575	0.4008	1.8	-0.0933	3.5044	-0.1643	0.5185	-0.7824	-0.139	-0.2921	-0.2145	0.6206	0.5805	0.0667	0.911	0.7139	0.1832	1.3977	0.2109	0.9671	-14.5875	-24.8627	-29.6777
10	6.4394	-0.6502	-1.3395	1.417	0.0977	0.279	0.1699	-0.4726	-0.3287	0.2539	-0.4133	-0.3741	0.4326	0.4458	0.1794	0.2	0.0456	-0.165	0.5004	0.0109	0.1883	-28.2831	-9.0779	-7.5052
11	2.6179	0.1894	0.9321	1.8926	0.5243	2.4999	0.0153	-0.0224	0.2521	0.2692	-0.0704	0.1936	0.0851	-0.1455	0.0924	0.1972	0.0478	-0.0389	0.0432	-0.0616	0.0828	-46.6908	-5.137	-18.9679
12	0.7276	-0.2755	-0.1273	0.3282	-0.2467	0.408	0.0038	-0.0775	-0.0318	0.445	-0.1565	0.0302	0.1977	0.0254	0.0894	0.1697	-0.2229	0.0955	-0.1486	0.0883	0.376	-48.7489	-13.8416	-21.3997
13	2.0521	-0.2031	0.5826	1.3103	-0.246	2.0335	-0.0646	0.0927	-0.2563	0.1356	0.0265	0.1674	0.1822	0.1908	0.0264	0.2627	-0.0033	-0.0514	0.0617	-0.0185	0.1761	-45.7503	-7.0032	-18.6027
14	1.8374	0.7288	0.3549	2.608	0.5457	1.777	0.134	-0.2135	0.2029	0.5346	-0.2105	0.6639	-0.1936	-0.284	-0.0063	0.2687	-0.0122	0.0996	0.1131	0.0407	0.5124	-52.3359	-6.1982	-11.056
15	3.5859	-0.5327	-1.7303	3.2013	0.5132	3.1206	0.102	-0.5554	0.3041	-0.3451	0.0901	-0.6893	-0.4804	0.9443	0.0224	0.511	-0.2231	0.2071	0.6352	0.1251	0.3384	-20.4373	-8.2884	-43.4597
16	0.815	-0.4854	0.3335	1.0734	-0.388	0.1813	-0.862	-0.3253	-0.1479	-0.0862	0.3249	-0.9865	0.1989	1.705	-0.2465	0.432	0.215	0.0819	1.5961	-0.076	0.6334	-9.863	-12.5499	-41.001
17	0.7465	-0.0798	0.5669	1.8799	0.9276	0.9421	-0.5128	-0.5177	-0.5468	-0.3909	0.0652	-0.616	1.0303	1.856	0.1361	0.6337	0.3598	0.2591	1.1321	0.1027	0.6255	-14.3842	-18.8824	-43.5345
18	0.2546	0.7998	-0.1878	2.8738	0.2603	2.2817	-0.1404	-0.5073	-0.6476	0.2655	0.1737	-0.5826	0.9716	1.2954	-0.0947	0.5345	0.1789	0.0394	1.0189	-0.0739	0.3271	-21.4077	-15.6104	-39.905

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 100 through 119 )	H	100 - 119
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 120 through 167 )	H	120 - 167
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 168 through 195 )	H	168 - 195
4	X-RAY DIFFRACTION	4	chain 'H' and (resid 196 through 223 )	H	196 - 223
5	X-RAY DIFFRACTION	5	chain 'L' and (resid 1 through 18 )	L	1 - 18
6	X-RAY DIFFRACTION	6	chain 'L' and (resid 19 through 38 )	L	19 - 38
7	X-RAY DIFFRACTION	7	chain 'L' and (resid 39 through 61 )	L	39 - 61
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 62 through 90 )	L	62 - 90
9	X-RAY DIFFRACTION	9	chain 'L' and (resid 91 through 102 )	L	91 - 102
10	X-RAY DIFFRACTION	10	chain 'L' and (resid 103 through 114 )	L	103 - 114
11	X-RAY DIFFRACTION	11	chain 'L' and (resid 115 through 151 )	L	115 - 151
12	X-RAY DIFFRACTION	12	chain 'L' and (resid 152 through 164 )	L	152 - 164
13	X-RAY DIFFRACTION	13	chain 'L' and (resid 165 through 199 )	L	165 - 199
14	X-RAY DIFFRACTION	14	chain 'L' and (resid 200 through 215 )	L	200 - 215
15	X-RAY DIFFRACTION	15	chain 'H' and (resid 1 through 17 )	H	1 - 17
16	X-RAY DIFFRACTION	16	chain 'H' and (resid 18 through 39 )	H	18 - 39
17	X-RAY DIFFRACTION	17	chain 'H' and (resid 40 through 83 )	H	40 - 83
18	X-RAY DIFFRACTION	18	chain 'H' and (resid 84 through 99 )	H	84 - 99

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