PDB-9n7o: Designed anti-OSM Fab

ID or keywords:

Entry

Database: PDB / ID: 9n7o

Title

Designed anti-OSM Fab

Components

(designed Fab ...) x 2

Keywords

IMMUNE SYSTEM / machine learning / antibody / design

Function / homology

DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL

Function and homology information

Biological species

Rattus norvegicus (Norway rat)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.48 Å

Authors

Kiefer, J.R. / Alberstein, R.G. / Hofmann, J.L. / Watkins, A.M. / Seeger, F. / Dou, Y. / Zhang, X.

Funding support

1items

Citation

Journal: To Be Published
Title: Lab-in-the-loop therapeutic antibody design with deep learning
Authors: Frey, N.C. / Hofmann, J.L. / Kiefer, J.R. / Alberstein, R.G. / Seeger, F. / Watkins, A.M. / Bonneau, R.

History

Deposition	Feb 6, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 11, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9n7o.cif.gz	219.8 KB	Display	PDBx/mmCIF format
PDB format	pdb9n7o.ent.gz	175.4 KB	Display	PDB format
PDBx/mmJSON format	9n7o.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/n7/9n7o ftp://data.pdbj.org/pub/pdb/validation_reports/n7/9n7o	HTTPS FTP

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Related structure data

Related structure data	9n2vC 9n7mC 9muy PDB Unreleased entry 9muz PDB Unreleased entry 9mvj PDB Unreleased entry 9mzc PDB Unreleased entry 9mzv PDB Unreleased entry C: citing same article (ref.)
Similar structure data	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

H: designed Fab heavy chain

L: designed Fab light chain

hetero molecules

48.2 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)	127.080, 127.080, 68.490
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

Components on special symmetry positions

ID	Model	Components
1	1	H-701- HOH

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Antibody , 2 types, 2 molecules HL

#1: Antibody	designed Fab heavy chain Mass: 24461.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody	designed Fab light chain Mass: 23127.600 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Cricetulus griseus (Chinese hamster)

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Non-polymers , 5 types, 624 molecules

#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 617 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.91 Å³/Da / Density % sol: 57.66 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 0.1 M Bis-Tris propane, pH 9.0, 10% v/v PEG200, 18% w/v PEG8000

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Data collection

Diffraction	Mean temperature: 93 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
Detector	Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Sep 12, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 1.48→44.93 Å / Num. obs: 94102 / % possible obs: 100 % / Redundancy: 26.1 % / CC_1/2: 0.999 / R_merge(I) obs: 0.182 / R_pim(I) all: 0.036 / R_rim(I) all: 0.186 / Χ²: 1 / Net I/σ(I): 13 / Num. measured all: 2455205
Reflection shell	Resolution: 1.48→1.5 Å / % possible obs: 100 % / Redundancy: 21.1 % / R_merge(I) obs: 1.858 / Num. measured all: 97460 / Num. unique obs: 4610 / CC_1/2: 0.306 / R_pim(I) all: 0.412 / R_rim(I) all: 1.904 / Χ²: 0.95 / Net I/σ(I) obs: 2

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Processing

Software

Name	Version	Classification
PHENIX	(1.21.2_5419: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.48→31.77 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.08 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2046	4649	4.94 %
R_work	0.1715	-	-
obs	0.1731	94027	99.92 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.48→31.77 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3336	0	37	617	3990

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	3626
X-RAY DIFFRACTION	f_angle_d	0.841	4945
X-RAY DIFFRACTION	f_dihedral_angle_d	12.813	1320
X-RAY DIFFRACTION	f_chiral_restr	0.085	546
X-RAY DIFFRACTION	f_plane_restr	0.006	646

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.48-1.49	0.3675	146	0.3524	2959	X-RAY DIFFRACTION	100
1.49-1.51	0.3535	134	0.346	2954	X-RAY DIFFRACTION	100
1.51-1.53	0.354	151	0.337	2952	X-RAY DIFFRACTION	100
1.53-1.55	0.3525	169	0.3146	2925	X-RAY DIFFRACTION	100
1.55-1.57	0.3032	161	0.3019	2940	X-RAY DIFFRACTION	100
1.57-1.59	0.2836	153	0.2907	2947	X-RAY DIFFRACTION	100
1.59-1.61	0.3346	156	0.2692	2924	X-RAY DIFFRACTION	100
1.61-1.64	0.316	171	0.2593	2945	X-RAY DIFFRACTION	100
1.64-1.66	0.2838	162	0.2536	2922	X-RAY DIFFRACTION	100
1.66-1.69	0.2455	144	0.236	2960	X-RAY DIFFRACTION	100
1.69-1.72	0.2561	183	0.2257	2955	X-RAY DIFFRACTION	100
1.72-1.75	0.2354	154	0.2136	2920	X-RAY DIFFRACTION	100
1.75-1.78	0.2646	146	0.2107	2966	X-RAY DIFFRACTION	100
1.78-1.82	0.2513	144	0.2045	2964	X-RAY DIFFRACTION	100
1.82-1.86	0.243	156	0.2001	2959	X-RAY DIFFRACTION	100
1.86-1.9	0.2194	158	0.183	2975	X-RAY DIFFRACTION	100
1.9-1.95	0.2314	142	0.179	2973	X-RAY DIFFRACTION	100
1.95-2	0.2244	155	0.1664	2969	X-RAY DIFFRACTION	100
2-2.06	0.2057	160	0.1605	2950	X-RAY DIFFRACTION	100
2.06-2.13	0.1642	156	0.1569	2967	X-RAY DIFFRACTION	100
2.13-2.21	0.1674	147	0.1535	2993	X-RAY DIFFRACTION	100
2.21-2.29	0.1985	159	0.1495	2981	X-RAY DIFFRACTION	100
2.29-2.4	0.1832	151	0.1603	2993	X-RAY DIFFRACTION	100
2.4-2.52	0.2133	141	0.1646	3002	X-RAY DIFFRACTION	100
2.52-2.68	0.194	159	0.1552	2996	X-RAY DIFFRACTION	100
2.68-2.89	0.1762	146	0.153	3020	X-RAY DIFFRACTION	100
2.89-3.18	0.2111	156	0.1553	3032	X-RAY DIFFRACTION	100
3.18-3.64	0.1877	143	0.1324	3055	X-RAY DIFFRACTION	100
3.64-4.58	0.1427	176	0.1133	3060	X-RAY DIFFRACTION	100
4.58-31.77	0.1543	170	0.1368	3220	X-RAY DIFFRACTION	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	1.1319	-0.3179	0.1446	2.2752	0.0995	1.0266	0.0765	-0.0142	0.0129	0.0509	-0.053	0.0157	0.1017	-0.0668	-0.0044	0.1503	-0.0343	-0.0589	0.1086	0.0238	0.0825	19.4537	9.0323	-24.1904
2	0.9924	0.1718	1.2046	3.08	0.5973	2.0621	0.2084	0.1734	-0.1758	-0.1759	-0.1868	0.1175	0.2611	-0.0636	-0.0724	0.1912	-0.0478	-0.0625	0.1236	0.0225	0.1045	18.6315	1.7633	-28.1527
3	0.265	0.2762	-0.4871	1.9916	-0.0561	-0.0995	-0.024	-0.0148	0.0156	0.0819	0.0098	-0.037	-0.0183	0.0399	0.0095	0.186	-0.0167	-0.0926	0.1349	0.0164	0.0975	26.5453	1.2623	-15.7961
4	2.4811	0.1224	0.7041	2.1715	-0.0283	2.0215	-0.0959	-0.3607	0.1373	0.48	-0.0068	0.0094	-0.0899	-0.1199	0.108	0.2513	0.0138	-0.0534	0.1584	-0.0121	0.0975	27.7322	-12.8913	-2.9036
5	1.8959	-1.1865	0.3735	3.5903	-1.6708	5.2295	0.2874	0.4335	-0.2031	-0.1686	-0.196	-0.4083	0.2308	0.6415	-0.2673	0.1061	0.0088	-0.042	0.1857	-0.0182	0.2249	47.9626	9.5856	-20.7227
6	4.0982	-0.8859	0.4817	2.9591	-0.7936	4.1605	0.1301	0.3066	0.2473	-0.0668	-0.1136	-0.2524	-0.2485	0.2951	0.0215	0.1528	-0.0321	-0.0343	0.1279	-0	0.1515	41.9365	17.0338	-22.5611
7	3.2587	-0.63	0.7243	3.0845	0.696	2.9952	-0.0414	-0.1794	-0.0743	0.2676	0.0414	-0.1929	-0.075	0.1619	0.0489	0.1394	-0.0202	-0.055	0.127	0.0099	0.1262	39.2577	18.4674	-14.1738
8	0.696	-0.5596	1.3859	4.4759	-3.1939	4.0979	0.0397	0.01	0.0328	0.376	-0.1539	-0.3926	-0.2664	0.3069	0.1231	0.1732	-0.0528	-0.0767	0.1954	0.0153	0.2326	46.7738	14.5003	-13.0663
9	0.3629	0.0338	-0.2887	2.0527	-0.6824	0.2912	-0.0109	-0.0163	0.0075	0.1145	-0.0826	-0.3038	-0.0439	0.0296	0.0427	0.164	-0.0231	-0.0985	0.1558	0.0084	0.1086	38.8942	-2.7766	-12.6485
10	1.5712	3.2693	0.3414	7.8452	1.0025	0.757	-0.1359	0.0162	0.0792	-0.007	-0.0653	-0.571	-0.1313	0.1405	0.1574	0.183	-0.0237	-0.104	0.1889	0.0836	0.1847	45.3771	-17.3123	-6.2213
11	1.2107	0.7941	-0.1486	5.343	-0.6533	1.2801	-0.1194	0.1987	0.1116	-0.2571	-0.3642	-0.8928	0.1478	0.2295	0.1628	0.1618	0.0162	-0.0155	0.219	0.0793	0.2073	44.7865	-25.016	-11.0916
12	3.5864	0.8234	-0.2497	1.9816	1.8651	3.8835	0.0901	-0.0859	0.3581	0.1654	-0.1417	-0.0878	-0.2727	0.0679	0.2817	0.2708	-0.047	-0.1305	0.1691	0.0646	0.2664	43.0999	-0.5657	-4.471
13	1.663	2.492	0.4372	8.9803	-0.6119	1.9166	-0.064	0.0541	-0.013	-0.2157	0.028	-0.3032	0.1692	0.1128	0.0806	0.1365	0.0291	-0.0268	0.1285	0.0146	0.1163	36.8283	-29.0616	-8.2737
14	2.4443	2.2441	0.4345	5.1352	0.1089	0.8345	0.0168	-0.203	0.1184	0.3983	-0.2593	-0.5203	0.0071	0.1868	0.0014	0.2024	0.0045	-0.1213	0.2052	0.0468	0.2465	46.6637	-24.5368	-0.2078

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'H' and (resid 1 through 75 )
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 76 through 87 )
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 88 through 134 )
4	X-RAY DIFFRACTION	4	chain 'H' and (resid 135 through 217 )
5	X-RAY DIFFRACTION	5	chain 'L' and (resid 1 through 17 )
6	X-RAY DIFFRACTION	6	chain 'L' and (resid 18 through 39 )
7	X-RAY DIFFRACTION	7	chain 'L' and (resid 40 through 69 )
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 70 through 83 )
9	X-RAY DIFFRACTION	9	chain 'L' and (resid 84 through 128 )
10	X-RAY DIFFRACTION	10	chain 'L' and (resid 129 through 150 )
11	X-RAY DIFFRACTION	11	chain 'L' and (resid 151 through 163 )
12	X-RAY DIFFRACTION	12	chain 'L' and (resid 164 through 174 )
13	X-RAY DIFFRACTION	13	chain 'L' and (resid 175 through 188 )
14	X-RAY DIFFRACTION	14	chain 'L' and (resid 189 through 214 )

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Antibody , 2 types, 2 molecules HL

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