PDB-3fo1: Crystal structure of hapten complex of catalytic elimination anti...

ID or keywords:

Entry

Database: PDB / ID: 3fo1

Title

Crystal structure of hapten complex of catalytic elimination antibody 13G5 (Glu(L39)Ala mutant)

Components

Catalytic antibody Fab 13G5 IgG2b heavy chain chimera
Catalytic antibody Fab 13G5 kappa light chain chimera

Keywords

IMMUNE SYSTEM / IMMUNOGLOBULIN / CATALYTIC ANTIBODY / CHIMERIC FAB / HAPTEN COMPLEX / ACID BASE CATALYSIS / PROTON TRANSFER / Immunoglobulin domain

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-BZH

Function and homology information

Biological species

Mus musculus (house mouse)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Debler, E.W. / Wilson, I.A.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: An aspartate and a water molecule mediate efficient acid-base catalysis in a tailored antibody pocket.
Authors: Debler, E.W. / Muller, R. / Hilvert, D. / Wilson, I.A.

History

Deposition	Dec 27, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 10, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Oct 20, 2021	Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Sep 6, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5	Nov 27, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3fo1.cif.gz	178 KB	Display	PDBx/mmCIF format
PDB format	pdb3fo1.ent.gz	142 KB	Display	PDB format
PDBx/mmJSON format	3fo1.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/fo/3fo1 ftp://data.pdbj.org/pub/pdb/validation_reports/fo/3fo1	HTTPS FTP

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Related structure data

Related structure data	3fo0C 3fo2C 2gjzS 2gk0 C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3fo2-d 5jw5-d 5mp6-d 4fa6-d 4aof-d 3t8m-d 6azx-d 4ps7-d 3ixt-d 4urk-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: Catalytic antibody Fab 13G5 kappa light chain chimera

H: Catalytic antibody Fab 13G5 IgG2b heavy chain chimera

A: Catalytic antibody Fab 13G5 kappa light chain chimera

B: Catalytic antibody Fab 13G5 IgG2b heavy chain chimera

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

2

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	59.602, 87.021, 84.401
Angle α, β, γ (deg.)	90.00, 91.34, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	L
2	1	A
1	2	L
2	2	A
1	3	H
2	3	B
1	4	H
2	4	B
1	5	H
2	5	B

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	6	A	1 - 107
2	1	1	6	A	1 - 107
1	1	2	6	A	108 - 211
2	1	2	6	A	108 - 211
1	1	3	6	H	1 - 113
2	1	3	6	B	1 - 113
1	1	4	6	H	114 - 126
2	1	4	6	B	114 - 126
1	1	5	6	H	136 - 227
2	1	5	6	B	136 - 227

NCS ensembles :

ID
1
2
3
4
5

#1: Antibody	Catalytic antibody Fab 13G5 kappa light chain chimera Mass: 23944.758 Da / Num. of mol.: 2 / Mutation: E39A Source method: isolated from a genetically manipulated source Details: The variable domain (residues 1-107) is from murine source and the constant domain (residues 108-214) is from human source Source: (gene. exp.) Mus musculus, Homo sapiens / Plasmid: p4xH-M13 / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP2
#2: Antibody	Catalytic antibody Fab 13G5 IgG2b heavy chain chimera Mass: 24296.205 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The variable domain (residues 1-113) is from murine source and the constant domain (residues 114-235) is from human source Source: (gene. exp.) Mus musculus, Homo sapiens / Plasmid: p4xH-M13 / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP2
#3: Chemical	ChemComp-BZH / 5-[(2-AMINO-1H-BENZIMIDAZOL-6-YL)AMINO]-5-OXOPENTANOIC ACID Mass: 262.265 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₂H₁₄N₄O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y
Sequence details	THE SEQUENCES OF THE FAB COMPLEXES ARE NOT AVAILABLE IN ANY SEQUENCE DATABASES.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.27 Å³/Da / Density % sol: 45.75 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 25% PEG 3350, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
Detector	Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 4, 2006 / Details: FLAT COLLIMATING MIRROR, TOROID FOCUSING MIRROR
Radiation	Monochromator: DOUBLE CRYSTAL Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.2→50 Å / Num. obs: 43563 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / R_sym value: 0.072 / Net I/σ(I): 22.3
Reflection shell	Resolution: 2.2→2.25 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.4 / R_sym value: 0.506 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
MAR345	CCD	data collection
PHASER		phasing
REFMAC	5.2.0019	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 2GJZ

2gjz

Resolution: 2.2→42.84 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.922 / SU B: 17.909 / SU ML: 0.237 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.345 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.28139	2256	5.2 %	RANDOM
R_work	0.22496	-	-	-
obs	0.22786	41378	99.69 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 27.708 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.04 Å²	-0 Å²	-0.06 Å²
2-	-	-3.6 Å²	0 Å²
3-	-	-	-0.44 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→42.84 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6540	0	38	165	6743

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	6748
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	4473
X-RAY DIFFRACTION	r_angle_refined_deg	1.421	1.961	9195
X-RAY DIFFRACTION	r_angle_other_deg	0.885	3.004	10949
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.792	5	856
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.035	24.724	254
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.52	15	1065
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.331	15	18
X-RAY DIFFRACTION	r_chiral_restr	0.082	0.2	1033
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	7482
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1286
X-RAY DIFFRACTION	r_nbd_refined	0.196	0.2	1069
X-RAY DIFFRACTION	r_nbd_other	0.199	0.2	4208
X-RAY DIFFRACTION	r_nbtor_refined	0.179	0.2	3038
X-RAY DIFFRACTION	r_nbtor_other	0.087	0.2	3680
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.159	0.2	245
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.183	0.2	7
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.169	0.2	29
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.192	0.2	5
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.658	1.5	5471
X-RAY DIFFRACTION	r_mcbond_other	0.125	1.5	1741
X-RAY DIFFRACTION	r_mcangle_it	0.785	2	6943
X-RAY DIFFRACTION	r_scbond_it	1.343	3	2990
X-RAY DIFFRACTION	r_scangle_it	1.921	4.5	2252
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	1461	loose positional	0.25	5
2	A	1359	loose positional	0.23	5
3	H	1544	loose positional	0.11	5
4	H	155	loose positional	0.38	5
5	H	973	loose positional	0.23	5
1	A	1461	loose thermal	0.73	10
2	A	1359	loose thermal	1.29	10
3	H	1544	loose thermal	1	10
4	H	155	loose thermal	1.93	10
5	H	973	loose thermal	0.82	10

LS refinement shell

Resolution: 2.2→2.26 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.371	162	-
R_work	0.284	2981	-
obs	-	-	98.65 %

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	1.2066	-1.0299	-0.4236	18.0608	-3.1853	0.8809	-0.131	-0.138	0.1265	0.1981	0.2166	-0.0837	0.3149	0.303	-0.0856	0.2644	0.0128	-0.0224	0.1846	0.0098	0.0473	38.5186	9.2498	17.0299
2	1.5338	0.4885	-0.2753	1.1757	0.4663	1.7891	0.0734	-0.1052	0.231	-0.2481	-0.0301	-0.1723	0.0021	0.0871	-0.0433	0.2557	0.0066	0.032	0.1073	-0.0048	0.0529	39.8384	5.5629	4.7341
3	2.203	-0.921	0.0117	9.4875	0.6598	2.1523	0.0241	-0.1429	0.0388	0.0383	-0.1481	-0.0965	-0.1932	0.1178	0.124	0.1791	-0.0055	0.0231	0.149	0.0149	-0.0213	36.4709	8.1688	10.7481
4	6.9872	0.6196	-0.843	2.2347	0.0143	1.7302	0.0661	0.0349	-0.0977	0.1252	-0.1485	0.482	-0.112	-0.2592	0.0825	0.2243	0.0109	0.0032	0.0776	-0.034	0.1259	9.8159	26.9452	19.5083
5	11.4215	2.5274	-3.232	0.5648	-0.6689	1.3022	-0.1686	-1.7567	-0.4869	0.0889	-0.1073	0.239	-0.0918	0.35	0.2759	0.2762	0.0468	0.038	0.2803	0.083	0.0518	9.8287	24.3394	30.8788
6	14.8918	0.6872	-5.228	1.7222	0.5602	2.9982	-0.3359	-0.1581	-0.0954	-0.0365	0.116	0.5148	0.4076	-0.0961	0.2199	0.1453	-0.0276	0.0319	0.1002	-0.0211	0.1878	11.8875	22.4331	20.001
7	17.4246	0.4276	1.182	2.783	0.8256	1.058	-0.3552	-0.6829	0.223	0.1696	0.0265	0.6371	0.0756	-0.1005	0.3287	0.2434	0.091	0.0118	0.2046	-0.1013	0.087	6.6564	32.1323	28.8761
8	5.6289	1.0722	-3.923	1.2366	-1.0146	4.022	0.1738	0.2617	0.3839	-0.3998	0.0616	0.4179	-0.1571	-0.2401	-0.2354	0.3138	0.0226	-0.0549	0.0667	-0.0128	0.0746	18.6717	-2.2091	-2.3508
9	5.7794	-1.5672	-1.2768	6.0216	1.2861	0.4399	0.0382	-0.7339	0.2542	0.2914	0.075	-0.308	-0.1098	0.099	-0.1132	0.1743	0.0117	-0.0279	0.1437	0.0193	0.068	24.4232	-1.831	9.5353
10	1.7074	0.2249	-0.8448	0.9726	0.1857	0.5277	-0.0319	-0.0334	-0.2187	0.0121	-0.1095	0.1701	-0.0216	-0.0406	0.1414	0.2695	0.0464	-0.034	0.0816	-0.004	0.0781	21.7851	-7.8253	1.8482
11	1.1375	-0.2677	-0.0983	1.4515	0.4463	0.3186	0.203	0.0109	0.0305	-0.1645	-0.1728	0.2247	-0.0044	-0.0556	-0.0303	0.2062	0.0275	-0.0176	0.1427	0.048	0.1358	15.6841	8.9809	5.9671
12	0.2743	1.0382	-0.6064	7.6919	-2.6124	1.3673	-0.0306	0.0067	-0.0936	-0.1928	0.0784	0.0217	-0.1841	-0.0453	-0.0479	0.1065	0.0016	-0.0286	0.1093	-0.0003	0.1572	7.9838	16.9048	11.4991
13	8.8626	9.5375	0.8336	10.2637	0.8971	0.0784	0.5079	-0.0397	1.3486	-0.0044	-0.7668	1.1133	0.9677	-0.2044	0.2589	0.4705	0.0396	-0.0457	0.0612	0.0262	0.2398	4.8447	32.2	3.6053
14	1.8066	0.3867	1.3186	32.917	-0.5617	4.6624	-0.0806	0.2322	0.5662	-1.6661	-0.0376	1.0875	0.0153	-0.3015	0.1182	0.0191	-0.0285	-0.1086	0.108	0.0252	0.2991	0.4761	16.7918	4.5712
15	2.0283	-0.2032	2.4807	1.0448	0.3323	3.4662	0.1349	-0.2618	-0.1644	0.277	0.1158	0.2613	0.3429	-0.335	-0.2507	0.313	-0.0455	0.0574	0.0934	0.0213	0.091	17.9538	-1.3383	43.2238
16	4.2356	0.9624	-0.9094	2.5365	-0.7465	0.321	-0.1337	0.2344	0.0429	-0.5665	0.1398	0.0044	-0.5065	0.0495	-0.0061	0.1697	0.042	-0.0105	0.1068	0.0509	0.0891	25.7756	1.8854	37.3573
17	1.5393	-0.414	0.3545	1.0418	-0.2066	0.4548	0.0094	0.0373	0.1872	0.0985	-0.0864	0.0746	-0.0932	0.0081	0.0769	0.2692	-0.0509	0.0224	0.0903	0.0024	0.0906	23.1505	3.1586	40.5012
18	0.7487	0.3897	0.3091	1.2593	0.0461	0.7703	0.0742	0.0684	-0.0743	0.1667	-0.0895	0.4228	0.2247	-0.0887	0.0154	0.1158	-0.0312	0.0568	0.1059	0.0003	0.197	7.5959	-17.7842	31.6618
19	0.5528	-0.3078	0.1766	5.0704	-1.6868	0.5715	-0.0716	0.0379	0.0694	0.2891	0.0892	-0.1507	0.1027	-0.0121	-0.0176	0.0854	-0.0214	0.0186	0.1357	-0.0124	0.1641	7.5188	-21.057	30.1333
20	3.3859	-6.656	-1.5929	17.8635	2.9247	0.7583	-0.0093	-0.0717	-0.7087	0.2145	-0.6874	1.1165	0.3093	-0.2385	0.6968	0.2886	-0.0866	-0.0139	0.0849	-0.0216	0.2597	3.1054	-34.9687	37.9668
21	5.1306	-6.0582	-0.644	12.0628	-3.6339	4.0142	0.0317	-0.6237	-0.3914	1.0103	-0.1062	1.5294	-0.4409	-0.3914	0.0746	0.1294	-0.0148	0.0847	0.1278	0.0501	0.2374	-0.4838	-20.0346	36.5867
22	2.7193	5.0352	2.1895	18.5701	1.7804	7.5382	-0.0729	0.0303	0.3411	0.2731	0.0407	0.6858	-0.0112	0.1585	0.0322	0.2684	0.0197	-0.0094	0.1923	0.0499	0.01	36.2584	-4.5702	24.8879
23	1.3401	5.5464	1.0952	23.5482	3.4692	2.8053	-0.0261	0.1915	-0.2956	-1.2151	-0.0268	-1.4141	-0.3495	0.0733	0.0529	0.0049	-0.0023	0.0618	0.2265	0.0205	0.182	39.9654	-18.0882	26.1526
24	1.0904	-0.1409	0.2002	1.9148	0.5132	2.4338	0.0377	-0.0288	-0.1158	0.1547	-0.0633	-0.2111	0.1916	0.1236	0.0255	0.193	0.0185	-0.019	0.1246	0.021	0.0843	39.0481	-9.1599	38.0878
25	1.5814	1.4769	-0.25	8.9471	0.9444	2.8182	-0.0292	0.045	-0.0682	0.0651	-0.0279	-0.2989	0.232	0.0567	0.0571	0.1493	0.0103	-0.0139	0.1644	0.028	0.0223	35.9871	-11.631	31.7912
26	5.3016	-0.6285	0.6643	2.0202	-0.0565	1.3321	0.0984	-0.0561	-0.0627	-0.165	-0.0843	0.3987	0.1135	-0.1834	-0.0141	0.2376	-0.0351	0.0115	0.0899	-0.0311	0.1195	9.6379	-30.2378	21.8516
27	7.7754	-0.8555	2.7898	1.8345	-1.3317	2.842	-0.232	0.8421	0.1253	-0.2683	0.1912	0.1472	0.1491	-0.1315	0.0408	0.3256	-0.0758	-0.0004	0.1503	0.0042	-0.0221	13.707	-26.9204	15.8466
28	3.7581	-1.1906	0.2356	1.8212	-0.191	1.0415	-0.3434	0.8757	-0.1556	-0.1844	0.0789	0.5153	0.0457	-0.1194	0.2645	0.3307	-0.115	-0.0325	0.1809	-0.0616	0.096	6.4463	-31.6988	14.3488

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 24
2	X-RAY DIFFRACTION	2	A	25 - 69
3	X-RAY DIFFRACTION	3	A	70 - 105
4	X-RAY DIFFRACTION	4	A	106 - 140
5	X-RAY DIFFRACTION	5	A	141 - 161
6	X-RAY DIFFRACTION	6	A	162 - 186
7	X-RAY DIFFRACTION	7	A	187 - 211
8	X-RAY DIFFRACTION	8	B	1 - 37
9	X-RAY DIFFRACTION	9	B	38 - 51
10	X-RAY DIFFRACTION	10	B	52 - 97
11	X-RAY DIFFRACTION	11	B	98 - 142
12	X-RAY DIFFRACTION	12	B	143 - 192
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