PDB-3ncj: Crystal structure of Fab15 Mut8

ID or keywords:

Entry

Database: PDB / ID: 3ncj

Title

Crystal structure of Fab15 Mut8

Components

Fab15 Mut8 heavy chain
Fab15 Mut8 light chain

Keywords

IMMUNE SYSTEM / antibody

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

FOURIER SYNTHESIS / Resolution: 1.6 Å

Authors

Luo, J. / Feng, Y. / Gilliland, G.L.

Citation

Journal: To be Published
Title: Co-evolution of antibody stability and Vk CDR-L3 canonical structure
Authors: Luo, J. / Feng, Y. / Gilliland, G.L.

History

Deposition	Jun 4, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 18, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Mar 31, 2021	Group: Derived calculations / Source and taxonomy Category: entity_src_gen / pdbx_struct_conn_angle ...entity_src_gen / pdbx_struct_conn_angle / struct_conn / struct_site Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3	Sep 6, 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	3ncj.cif.gz	199 KB	Display	PDBx/mmCIF format
PDB format	pdb3ncj.ent.gz	156.8 KB	Display	PDB format
PDBx/mmJSON format	3ncj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3ncj_validation.pdf.gz	462.8 KB	Display	wwPDB validaton report
Full document	3ncj_full_validation.pdf.gz	469.1 KB	Display
Data in XML	3ncj_validation.xml.gz	25.3 KB	Display
Data in CIF	3ncj_validation.cif.gz	38.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nc/3ncj ftp://data.pdbj.org/pub/pdb/validation_reports/nc/3ncj	HTTPS FTP

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Related structure data

Related structure data	3na9C 3naaSC 3nabC 3nacC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	1him-2 4q2z-2 3kym-8 3mck-1 4uim-2 1t3f-d 1nlb-d 4nm4-2 1dfb-d 4xxd-2 5my4-d 3ifp-2 6h06-1 6uoe-d 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: Fab15 Mut8 light chain

H: Fab15 Mut8 heavy 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

Unit cell

Length a, b, c (Å)	54.550, 74.700, 65.390
Angle α, β, γ (deg.)	90.00, 104.23, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Antibody , 2 types, 2 molecules LH

#1: Antibody	Fab15 Mut8 light chain Mass: 23249.838 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody	Fab15 Mut8 heavy chain Mass: 24501.354 Da / Num. of mol.: 1 / Mutation: V34I, G35S, E95Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)

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Non-polymers , 4 types, 627 molecules

#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 620 / 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: 2.7 Å³/Da / Density % sol: 54.52 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 0.1 sodium acetate, 7% PEG 5000, 0.2 M zinc acetate, 5% dioxane, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 93 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
Detector	Type: RIGAKU SATURN 944 / Detector: CCD / Date: Jun 3, 2010
Radiation	Monochromator: Osmic VariMax confocal optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 1.6→30 Å / Num. all: 60088 / Num. obs: 60088 / % possible obs: 89.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / B_iso Wilson estimate: 2.2 Å² / R_merge(I) obs: 0.061 / Net I/σ(I): 16
Reflection shell	Resolution: 1.6→1.66 Å / Redundancy: 1.1 % / R_merge(I) obs: 0.23 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3635 / % possible all: 53.9

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Processing

Software

Name	Version	Classification
StructureStudio		data collection
PHENIX	(phenix.refine: 1.6.1_357)	refinement
d*TREK		data reduction
d*TREK		data scaling

Refinement

Method to determine structure:

FOURIER SYNTHESIS
Starting model: PDB entry 3NAA

3naa

Resolution: 1.6→29.175 Å / SU ML: 0.23 / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / σ(F): 1.34 / σ(I): -3 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2245	3214	5.35 %	random
R_work	0.2004	-	-	-
obs	0.2017	60044	89.15 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 59.515 Å² / k_sol: 0.423 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.9106 Å²	-0 Å²	-2.5506 Å²
2-	-	3.346 Å²	-0 Å²
3-	-	-	-0.4354 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→29.175 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3357	0	18	620	3995

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	3499
X-RAY DIFFRACTION	f_angle_d	1.095	4759
X-RAY DIFFRACTION	f_dihedral_angle_d	12.621	1258
X-RAY DIFFRACTION	f_chiral_restr	0.077	531
X-RAY DIFFRACTION	f_plane_restr	0.005	607

LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection obs	% reflection obs (%)
1.6-1.6217	0.2259	68	0.2161	1203	1203	44
1.6217-1.647	0.2522	103	0.2177	1643	1643	60
1.647-1.674	0.2641	112	0.2117	2028	2028	73
1.674-1.7029	0.2263	128	0.1952	2312	2312	84
1.7029-1.7338	0.2027	128	0.1951	2402	2402	87
1.7338-1.7672	0.2215	146	0.1927	2463	2463	89
1.7672-1.8032	0.2353	140	0.1928	2487	2487	91
1.8032-1.8424	0.2082	135	0.1891	2540	2540	92
1.8424-1.8853	0.2218	147	0.1911	2598	2598	94
1.8853-1.9324	0.2008	150	0.1871	2643	2643	96
1.9324-1.9847	0.2243	159	0.1852	2723	2723	97
1.9847-2.043	0.1987	139	0.1773	2725	2725	99
2.043-2.109	0.1925	147	0.1751	2789	2789	100
2.109-2.1843	0.1967	161	0.1679	2759	2759	100
2.1843-2.2717	0.1891	162	0.1699	2748	2748	100
2.2717-2.3751	0.2007	163	0.1745	2774	2774	100
2.3751-2.5002	0.2062	135	0.181	2779	2779	100
2.5002-2.6568	0.2276	154	0.1822	2756	2756	100
2.6568-2.8618	0.1973	162	0.1767	2781	2781	100
2.8618-3.1495	0.1836	160	0.1807	2735	2735	99
3.1495-3.6045	0.2186	157	0.172	2548	2548	92
3.6045-4.5385	0.1991	134	0.198	2194	2194	78
4.5385-29.1796	0.2311	124	0.2177	2200	2200	77

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	0.8755	0.3795	0.2176	0.1696	0.1723	0.5217	0.1615	-0.0582	-0.558	0.2163	0.0663	-0.1656	0.2834	-0.0238	-0.1596	0.24	0.0078	-0.0608	0.1727	0.0005	0.2942	24.5066	-15.0378	29.9647
2	0.3239	0.258	0.51	0.313	0.185	1.4041	0.2984	-0.6158	-0.252	0.1186	-0.1554	0.0168	0.1021	-0.6182	-0.1899	0.2103	-0.0725	-0.0206	0.3424	0.0952	0.1702	10.8294	-10.6148	33.5543
3	1.3546	0.8476	0.5755	0.6891	0.351	0.385	0.1992	-0.3685	-0.0754	0.2143	-0.1914	-0.0486	0.129	-0.2834	-0.0151	0.22	-0.0548	-0.0029	0.2809	0.0518	0.1365	24.0792	-4.5218	39.4766
4	0.4252	0.3089	0.4647	0.4842	0.293	0.7624	0.1875	-0.2793	-0.2011	0.1381	-0.0928	-0.045	0.0441	-0.1408	-0.064	0.1882	-0.0446	-0.0114	0.2441	0.0558	0.1434	22.8057	-6.7574	34.722
5	0.8829	0.17	0.6263	0.5998	-0.4087	0.8611	-0.0032	0.0703	-0.0293	-0.2057	0.079	0.1511	0.1981	-0.0369	-0.0599	0.1505	0.0039	-0.0034	0.1025	-0.0004	0.1222	2.7904	-2.9983	0.381
6	0.7675	-0.1023	0.036	0.601	-0.2573	0.1913	0.0463	0.5821	0.1451	-0.1468	-0.0209	-0.1738	-0.3346	-0.058	-0.0388	0.2256	-0.0346	0.0293	0.2509	0.0356	0.1576	12.1025	-0.3814	-8.0107
7	0.7958	0.227	0.0673	0.2756	0.1193	0.2222	0.0595	-0.1039	-0.0449	-0.0296	0.0113	-0.0766	-0.0387	0.0438	-0.0522	0.115	0.0071	0.0167	0.0978	-0.0006	0.1306	10.023	-5.6447	7.6202
8	0.2751	-0.2923	0.0707	0.5994	0.1098	0.1897	0.2435	0.3484	0.07	-0.776	-0.1779	0.0521	0.6094	0.3229	-0.0874	0.5015	-0.0105	-0.0036	0.3535	-0.0488	0.125	13.1526	-6.7424	-13.7305
9	0.4119	0.1026	0.1086	0.6281	0.2563	0.7604	0.0195	0.0206	-0.1689	-0.1007	0.1245	0.0236	0.1521	0.0526	-0.1775	0.2013	0.0016	0.0008	0.075	0.0015	0.1813	6.0429	-13.7666	3.5613
10	0.6417	0.5291	-0.9107	2.6923	0.8163	2.4409	0.3813	-0.0657	-0.181	0.2956	-0.1393	-0.181	0.7895	-1.1539	-0.1458	0.3023	-0.1155	-0.0745	0.3392	0.0329	0.2496	-2.8789	-2.8383	-11.247
11	0.6425	-0.1382	-0.1457	0.5227	-0.2986	1.3778	0.0792	0.0509	0.1448	0.1498	0.1497	-0.0269	-0.461	-0.2673	-0.1586	0.2208	0.0475	0.0092	0.1913	0.0078	0.1628	30.7222	12.124	24.5366
12	0.7744	-0.1373	-0.2966	0.5426	-0.0316	1.6798	-0.073	0.1274	0.0391	0.1414	-0.1573	0.0825	-0.4092	-0.0451	0.1714	0.2194	-0.0348	-0.0014	0.1318	-0.0003	0.1582	38.2742	11.1209	21.3505
13	0.5157	0.3404	0.3573	0.7766	-0.173	1.545	0.0823	-0.1439	-0.0835	0.0466	-0.0872	-0.1151	0.0218	-0.4528	0.022	0.1506	-0.0393	-0.0061	0.1585	-0.0044	0.122	35.1822	3.5274	28.881
14	1.7005	0.1514	0.0463	1.813	0.2617	1.0176	-0.2171	0.1889	0.1478	0.1444	0.3523	-0.0636	0.1807	-0.0223	-0.0714	0.168	-0.0427	0.0024	0.1559	0.0234	0.1477	33.3959	-4.5289	24.7623
15	0.5478	0.1361	-0.2389	0.4187	-0.06	1.0739	-0.0127	-0.006	0.0257	0.0682	-0.0615	-0.0822	-0.1292	0.0632	0.061	0.1502	-0.0096	-0.0011	0.1462	0.0024	0.1398	37.9916	4.1666	25.642
16	0.1433	-0.218	0.1926	0.3276	-0.4329	0.8481	-0.0271	0.2439	0.0301	-0.0759	0.0097	0.0204	0.0868	0.1701	0.0079	0.1088	0.0013	0.0177	0.1119	-0.0053	0.113	14.1503	4.6302	-1.0391
17	0.609	-0.4915	0.3093	0.3525	-0.3309	0.2592	-0.1014	0.0444	0.2155	-0.0044	0.0739	0.0516	0.0339	0.0873	0.0172	0.0818	0.0022	0.0077	0.1128	-0.0058	0.1274	12.9654	6.8847	2.6924
18	0.6024	0.0933	0.1703	0.7758	0.1429	0.4872	-0.1358	0.0117	0.1761	0.0557	0.137	-0.006	-0.2004	0.1636	-0.0287	0.1133	0.0125	-0.007	0.1037	-0.0147	0.1494	4.8928	15.0444	4.1128
19	0.4533	0.1175	-0.0441	0.1066	-0.0093	0.0853	-0.0227	-0.0067	-0.0249	-0.0105	0.0335	0.0188	-0.0587	0.0772	-0.0131	0.1008	0.0046	0.0093	0.1088	0.0102	0.125	8.9813	6.9951	2.1459
20	1.244	-0.0861	0.8747	0.7495	-0.1379	0.7199	-0.0327	0.2178	0.5911	-0.0279	-0.1702	0.0348	-0.0377	0.1201	0.137	0.1204	-0.0198	-0.0076	0.1088	0.0459	0.2203	10.2969	13.4846	-6.0042

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain H and resid 1:10)
2	X-RAY DIFFRACTION	2	(chain H and resid 11:23)
3	X-RAY DIFFRACTION	3	(chain H and resid 24:71)
4	X-RAY DIFFRACTION	4	(chain H and resid 72:113)
5	X-RAY DIFFRACTION	5	(chain H and resid 114:131)
6	X-RAY DIFFRACTION	6	(chain H and resid 132:141)
7	X-RAY DIFFRACTION	7	(chain H and resid 142:182)
8	X-RAY DIFFRACTION	8	(chain H and resid 183:192)
9	X-RAY DIFFRACTION	9	(chain H and resid 193:211)
10	X-RAY DIFFRACTION	10	(chain H and resid 212:217)
11	X-RAY DIFFRACTION	11	(chain L and resid 1:13)
12	X-RAY DIFFRACTION	12	(chain L and resid 14:27)
13	X-RAY DIFFRACTION	13	(chain L and resid 28:41)
14	X-RAY DIFFRACTION	14	(chain L and resid 42:47)
15	X-RAY DIFFRACTION	15	(chain L and resid 48:104)
16	X-RAY DIFFRACTION	16	(chain L and resid 105:125)
17	X-RAY DIFFRACTION	17	(chain L and resid 126:145)
18	X-RAY DIFFRACTION	18	(chain L and resid 146:161)
19	X-RAY DIFFRACTION	19	(chain L and resid 162:195)
20	X-RAY DIFFRACTION	20	(chain L and resid 196:214)

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Antibody , 2 types, 2 molecules LH

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Non-polymers , 4 types, 627 molecules

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