PDB-6amj: CAT192 Fab Wild Type

ID or keywords:

Entry

Database: PDB / ID: 6amj

Title

CAT192 Fab Wild Type

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 / DI(HYDROXYETHYL)ETHER

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.49 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 9, 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
Revision 1.4	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6amj.cif.gz	339 KB	Display	PDBx/mmCIF format
PDB format	pdb6amj.ent.gz	278.8 KB	Display	PDB format
PDBx/mmJSON format	6amj.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6amj_validation.pdf.gz	471.4 KB	Display	wwPDB validaton report
Full document	6amj_full_validation.pdf.gz	487.1 KB	Display
Data in XML	6amj_validation.xml.gz	35.2 KB	Display
Data in CIF	6amj_validation.cif.gz	49.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/am/6amj ftp://data.pdbj.org/pub/pdb/validation_reports/am/6amj	HTTPS FTP

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Related structure data

Related structure data	6ammC 6anpC 6ao0C 3skjS 4gszS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6ev1-2 5bvj-4 6amm-d 3drt-d 1rzi-3 3eo0-2 4yny-1 3wfh-d 2v7n-1 5cd3-3 3f12-1 6ev1-1 5jqd-1 5ysl-1 5i8e-2 2adi-d 4mqx-2 3nfs-d 3hc3-d 7lk9-1 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

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

H: CAT192 Fab heavy chain

B: CAT192 Fab heavy chain

hetero molecules

95.6 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

hetero molecules

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

Unit cell

Length a, b, c (Å)	55.950, 83.350, 104.910
Angle α, β, γ (deg.)	90.000, 104.770, 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: 24592.289 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: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.48 Å³/Da / Density % sol: 50.33 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 12% PEG 8K, 0.1M Sodium cacodylate pH 6.0, 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: Nov 24, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5419 Å / Relative weight: 1
Reflection	Resolution: 2.49→30.713 Å / Num. obs: 32712 / B_iso Wilson estimate: 35.55 Å²
Reflection shell	Resolution: 2.49→2.62 Å / Redundancy: 2.9 % / R_merge(I) obs: 0.396 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4715 / % possible all: 98.8

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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: 4GSZ, 3SKJ

4gsz

3skj

Resolution: 2.49→30.713 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.52 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2618	1992	6.09 %
R_work	0.2057	30720	-
obs	0.209	32712	99.75 %

Solvent computation

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

Displacement parameters

B_iso max: 123.34 Å² / B_iso mean: 45.2615 Å² / B_iso min: 10.37 Å²

Refinement step

Cycle: final / Resolution: 2.49→30.713 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6336	0	18	309	6663
B_iso mean	-	-	48.31	33.74	-
Num. residues	-	-	-	-	837

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	6488
X-RAY DIFFRACTION	f_angle_d	0.473	8826
X-RAY DIFFRACTION	f_chiral_restr	0.04	1005
X-RAY DIFFRACTION	f_plane_restr	0.003	1125
X-RAY DIFFRACTION	f_dihedral_angle_d	14.621	3872

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.49-2.5523	0.4176	137	0.3023	2138	2275	98
2.5523-2.6212	0.3425	143	0.2881	2179	2322	100
2.6212-2.6983	0.3494	143	0.2619	2178	2321	100
2.6983-2.7854	0.2928	146	0.2575	2204	2350	100
2.7854-2.8848	0.3113	143	0.253	2162	2305	100
2.8848-3.0003	0.3242	142	0.2397	2168	2310	100
3.0003-3.1367	0.323	138	0.2499	2218	2356	100
3.1367-3.3019	0.2713	144	0.2227	2193	2337	100
3.3019-3.5085	0.2741	140	0.2079	2202	2342	100
3.5085-3.7789	0.267	140	0.2073	2191	2331	100
3.7789-4.1584	0.2586	138	0.1845	2195	2333	100
4.1584-4.7582	0.2052	144	0.1534	2215	2359	100
4.7582-5.9875	0.1889	142	0.1563	2222	2364	100
5.9875-30.7156	0.2061	152	0.178	2255	2407	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	3.9021	-0.342	-2.2455	4.1044	-0.3376	1.3572	0.1794	-0.3385	-0.0252	0.5992	-0.0816	-0.3322	0.1843	0.8252	-0.1117	0.1714	-0.0254	-0.0259	0.3463	0.0784	0.334	106.97	81.9776	119.9271
2	2.7266	-0.1319	0.8807	3.2573	1.9147	7.3785	0.0957	-0.0014	0.2525	-0.026	0.0175	-0.7592	-0.217	1.0696	-0.0406	0.2071	-0.0273	-0.0911	0.4246	0.0457	0.4389	108.1906	85.0426	110.9935
3	4.2891	0.8908	-0.3064	4.6187	0.0182	4.688	-0.412	0.4092	0.8043	0.199	0.0592	-0.4662	-0.7324	0.2143	0.2362	0.3618	-0.1125	-0.0853	0.3233	0.0357	0.524	105.663	95.7661	115.5759
4	6.5337	1.6163	0.6961	8.4679	4.3486	7.2448	0.0567	-0.5327	0.0677	0.4179	-0.1085	-0.5461	-0.2515	1.4016	-0.1449	0.1737	-0.0511	-0.1003	0.514	0.0524	0.3804	113.723	86.7097	114.0324
5	2.2818	-1.5127	-1.9356	3.5425	-0.976	4.1426	0.1366	-0.3205	-0.0889	0.4492	-0.0214	-1.0682	-1.4341	0.3382	-0.237	0.3428	-0.1518	-0.0714	0.4493	-0.0543	0.4892	105.1974	90.3378	121.7135
6	2.1695	0.352	-0.1394	0.6632	-2.3487	8.729	0.1978	0.0212	0.2051	0.0653	-0.0587	-0.0559	0.0734	0.7158	-0.1673	0.205	0.0256	-0.0512	0.1233	-0.026	0.3292	101.4984	83.0133	120.127
7	2.0328	-0.48	1.9357	3.3755	1.8228	4.6557	-0.414	-0.3801	0.0532	0.5866	0.5347	1.4252	-0.0675	-0.9879	-0.1086	0.4411	0.125	0.1737	0.6626	0.3025	0.707	72.7326	72.6949	138.2368
8	6.9994	4.9693	-0.2229	6.1714	0.1271	3.5995	-0.1876	-0.2535	-0.1309	0.3304	0.3413	-0.1644	0.3794	-0.0926	-0.1536	0.3099	0.1217	0.0416	0.3088	0.0489	0.1736	87.6958	71.519	135.1269
9	3.7586	3.1948	-0.2548	7.2896	-1.8759	1.9147	-0.2449	-0.0881	0.0555	0.1754	0.5367	-0.0116	-0.0282	0.1289	-0.2551	0.3309	0.0862	0.009	0.3172	-0.0511	0.1831	88.5016	74.8564	132.6627
10	2.5557	0.6628	-1.4101	4.2662	-2.0249	3.9483	-0.0934	-0.0838	-0.1132	0.2031	0.5445	0.6824	0.2346	-0.6518	-0.5349	0.4036	0.1051	0.0359	0.4086	0.1164	0.3012	81.2263	65.2168	137.8024
11	4.5378	2.0311	-3.0082	2.9535	-0.4453	2.8711	-0.0911	-0.1026	0.2326	0.7272	0.3138	0.2804	-0.1298	0.1679	-0.3387	0.4564	0.1868	0.1205	0.387	0.0838	0.2595	93.3816	56.2494	146.2788
12	5.0203	0.0272	-1.5567	0.9022	0.3596	0.7438	0.1678	-0.3598	0.4108	0.3327	0.2766	0.2122	0.1177	-0.3757	-0.4178	0.7739	0.174	0.1753	0.64	0.3177	0.4194	86.4634	50.9182	150.1668
13	8.1484	-2.0984	3.2808	4.3701	-0.6847	4.9287	-0.2609	-0.765	-1.1984	0.4739	-0.1508	0.2484	0.5457	0.2387	0.046	0.6596	0.0921	0.0602	0.3972	0.1219	0.2944	95.0319	42.3845	151.1765
14	4.8533	0.7657	0.8205	3.3119	0.0287	5.5693	-0.1994	-0.754	0.034	0.7482	0.1165	0.3106	0.2883	-0.0734	0.0456	0.6405	0.1478	0.1316	0.4561	0.1651	0.3248	90.8772	49.6555	149.3034
15	7.8554	7.4798	-4.1091	9.099	-4.1783	2.1815	-0.3131	-0.372	0.256	-0.0348	0.126	-0.1591	-0.2812	0.1075	0.0313	0.3453	0.0417	-0.0784	0.4712	-0.0499	0.2171	107.4634	59.8281	138.3584
16	5.0268	1.7779	5.4898	5.015	2.631	6.7091	0.2443	0.2866	-0.4248	-0.5681	0.1764	-0.2211	0.8889	0.3234	-0.2139	0.3527	-0.0921	0.0257	0.2583	-0.0486	0.3368	105.5807	56.8554	108.47
17	3.4472	0.3581	2.3774	2.1723	-0.0303	2.9346	-0.1839	-0.0531	0.0698	0.4512	0.373	0.2034	-0.0362	-0.0989	-0.1457	0.2509	0.0284	-0.0208	0.2364	0.0138	0.2592	103.1665	62.5767	122.4395
18	1.0134	0.668	0.4989	4.0477	-2.4827	5.9907	0.3046	0.0238	-0.171	0.3275	0.1836	0.2635	0.3726	0.1617	-0.391	0.2517	0.0336	-0.0235	0.2138	-0.0561	0.2963	102.3143	59.2408	124.9666
19	1.5256	0.5471	0.5659	2.6292	-0.3908	6.6379	-0.2487	0.29	0.1379	-0.3082	0.0192	0.1621	0.4325	-0.5161	-0.1028	0.1692	-0.0504	-0.0344	0.2539	0.0304	0.2996	98.0203	61.0655	108.3149
20	2.0125	-0.0653	2.5734	4.2177	-0.7476	5.5697	-0.0001	0.3268	0.2658	-0.0639	0.0485	-0.0459	-0.3121	0.8255	0.0716	0.1467	-0.0162	0.0299	0.2912	0.0528	0.3604	106.3056	69.2372	115.5245
21	4.7331	1.413	-1.0215	7.0017	-1.725	6.0039	-0.0773	-0.7441	0.8057	0.0044	0.1729	0.3785	-0.1418	-0.7563	-0.1074	0.1689	0.0754	-0.0294	0.2024	0.0084	0.3056	81.1002	93.4857	107.5683
22	2.4338	1.8268	-1.2502	4.8862	-1.1107	3.65	0.2278	-0.283	0.8259	0.2273	-0.2715	-0.4055	-0.1983	0.3729	0.0112	0.2176	-0.021	0.0215	0.1648	0.0547	0.5441	90.6737	95.7447	104.905
23	2.9752	0.2116	0.4254	6.043	-0.6545	3.9312	-0.1349	0.2174	0.1779	-0.4838	0.0715	-0.0067	0.0264	-0.0438	0.0556	0.1882	0.0156	-0.0199	0.2483	0.14	0.4396	89.3751	92.8648	97.1349
24	6.4823	2.7107	1.2776	1.9653	-1.1792	3.9423	-0.007	-0.2915	-0.4221	-0.1563	-0.1002	-0.989	0.0759	0.1121	0.113	0.228	0.0527	-0.0333	0.1762	0.0384	0.4845	86.4572	87.7352	105.918
25	2.524	-1.1233	-1.0263	1.8388	-1.9089	4.3893	0.3719	-0.1298	0.2321	0.3344	-0.2713	-0.2508	-0.739	0.0984	-0.1357	0.2347	-0.0936	-0.0026	0.2846	-0.0335	0.3294	85.662	90.8321	111.5808
26	6.6691	0.907	0.9099	5.7498	0.8003	1.9269	0.3187	-1.2897	0.0895	0.7668	0.5814	0.6574	-0.0383	-0.4331	-0.0303	0.4179	0.2711	0.1379	0.5477	0.1356	0.4186	76.1017	78.2891	140.5509
27	3.8207	0.7986	-0.0916	1.6797	-0.6817	2.6118	-0.0719	-0.1889	0.9345	0.7054	0.3938	0.502	-0.4013	-0.3695	0.0766	0.3913	0.1831	0.075	0.2449	0.0735	0.5291	75.4448	87.8711	129.6172
28	3.3981	0.0761	-0.3238	2.2679	-0.5402	3.7654	-0.0461	-0.7496	0.4136	0.5217	0.3549	0.0148	-0.2045	-0.2377	-0.2022	0.3371	0.1496	0.0009	0.3667	-0.0364	0.2999	79.9105	83.0251	134.8842
29	2.9891	-0.1816	2.2395	0.8757	0.7351	2.8043	-0.4412	-0.2899	1.0897	0.6018	0.4255	-0.1565	-1.5453	-1.0326	0.3347	0.5955	0.2979	0.1144	0.5826	0.1334	0.6699	70.1302	89.3126	133.2794
30	3.6029	0.59	0.2499	1.0677	-0.4249	2.2302	-0.2244	-0.0156	-1.1345	0.3238	0.3652	0.7722	1.558	-0.7669	-0.2161	1.1457	-0.3037	0.3728	0.4754	0.3248	0.9107	82.4341	33.0502	137.5724
31	1.3395	-0.6852	-0.3063	2.0679	-0.5674	3.828	-0.1263	0.133	-0.1447	0.2395	0.4946	0.6073	0.9457	-0.9041	-0.3382	0.56	-0.1192	0.0215	0.3303	0.0531	0.4127	91.4291	41.3195	125.8467
32	5.5422	1.9616	0.0558	2.6711	0.9484	1.446	-0.1346	0.2475	-0.6112	-0.3001	0.1448	-0.3815	0.258	0.0736	-0.05	0.3551	0.039	-0.0202	0.1893	-0.0213	0.2467	108.0444	46.1299	116.1066

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 18 )	L	1 - 18
2	X-RAY DIFFRACTION	2	chain 'L' and (resid 19 through 38 )	L	19 - 38
3	X-RAY DIFFRACTION	3	chain 'L' and (resid 39 through 61 )	L	39 - 61
4	X-RAY DIFFRACTION	4	chain 'L' and (resid 62 through 75 )	L	62 - 75
5	X-RAY DIFFRACTION	5	chain 'L' and (resid 76 through 90 )	L	76 - 90
6	X-RAY DIFFRACTION	6	chain 'L' and (resid 91 through 113 )	L	91 - 113
7	X-RAY DIFFRACTION	7	chain 'L' and (resid 114 through 128 )	L	114 - 128
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 129 through 150 )	L	129 - 150
9	X-RAY DIFFRACTION	9	chain 'L' and (resid 151 through 174 )	L	151 - 174
10	X-RAY DIFFRACTION	10	chain 'L' and (resid 175 through 211 )	L	175 - 211
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 1 through 18 )	A	1 - 18
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 19 through 38 )	A	19 - 38
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 39 through 61 )	A	39 - 61
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 62 through 102 )	A	62 - 102
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 103 through 113 )	A	103 - 113
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 114 through 128 )	A	114 - 128
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 129 through 150 )	A	129 - 150
18	X-RAY DIFFRACTION	18	chain 'A' and (resid 151 through 174 )	A	151 - 174
19	X-RAY DIFFRACTION	19	chain 'A' and (resid 175 through 188 )	A	175 - 188
20	X-RAY DIFFRACTION	20	chain 'A' and (resid 189 through 214 )	A	189 - 214
21	X-RAY DIFFRACTION	21	chain 'H' and (resid 1 through 17 )	H	1 - 17
22	X-RAY DIFFRACTION	22	chain 'H' and (resid 18 through 44 )	H	18 - 44
23	X-RAY DIFFRACTION	23	chain 'H' and (resid 45 through 83 )	H	45 - 83
24	X-RAY DIFFRACTION	24	chain 'H' and (resid 84 through 99 )	H	84 - 99
25	X-RAY DIFFRACTION	25	chain 'H' and (resid 100 through 129 )	H	100 - 129
26	X-RAY DIFFRACTION	26	chain 'H' and (resid 130 through 153 )	H	130 - 153
27	X-RAY DIFFRACTION	27	chain 'H' and (resid 154 through 167 )	H	154 - 167
28	X-RAY DIFFRACTION	28	chain 'H' and (resid 168 through 204 )	H	168 - 204
29	X-RAY DIFFRACTION	29	chain 'H' and (resid 205 through 222 )	H	205 - 222
30	X-RAY DIFFRACTION	30	chain 'B' and (resid 3 through 60 )	B	3 - 60
31	X-RAY DIFFRACTION	31	chain 'B' and (resid 61 through 153 )	B	61 - 153
32	X-RAY DIFFRACTION	32	chain 'B' and (resid 154 through 224 )	B	154 - 224

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