PDB-2uyl: Crystal structure of a monoclonal antibody directed against an an...

ID or keywords:

Entry

Database: PDB / ID: 2uyl

Title

Crystal structure of a monoclonal antibody directed against an antigenic determinant common to Ogawa and Inaba serotypes of Vibrio cholerae O1

Components

(MONOCLONAL ANTIBODY F-22-30) x 2

Keywords

IMMUNE SYSTEM / FAB FRAGMENT / MONOCLONAL ANTIBODY / IMMUNOGLOBULIN DOMAIN / IMMUNOGLOBULIN C REGION / ANTI-LPS VIBRIO CHOLERAE

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta

Function and homology information

Biological species

MUS MUSCULUS (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Ahmed, F. / Haouz, A. / Nato, F. / Fournier, J.M. / Alzari, P.M.

Citation

Journal: Proteins / Year: 2008
Title: Crystal Structure of a Monoclonal Antibody Directed Against an Antigenic Determinant Common to Ogawa and Inaba Serotypes of Vibrio Cholerae O1.
Authors: Ahmed, F. / Andre-Leroux, G. / Haouz, A. / Boutonnier, A. / Delepierre, M. / Qadri, F. / Nato, F. / Fournier, J.M. / Alzari, P.M.

History

Deposition	Apr 10, 2007	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 13, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Jun 6, 2012	Group: Other
Revision 1.3	May 1, 2024	Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Remark 700

SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2uyl.cif.gz	319.8 KB	Display	PDBx/mmCIF format
PDB format	pdb2uyl.ent.gz	261.2 KB	Display	PDB format
PDBx/mmJSON format	2uyl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2uyl_validation.pdf.gz	468 KB	Display	wwPDB validaton report
Full document	2uyl_full_validation.pdf.gz	505.6 KB	Display
Data in XML	2uyl_validation.xml.gz	57.2 KB	Display
Data in CIF	2uyl_validation.cif.gz	79.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uy/2uyl ftp://data.pdbj.org/pub/pdb/validation_reports/uy/2uyl	HTTPS FTP

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Related structure data

Similar structure data	4dn3-d 5vz1-2 5dq9-1 3gnm-d 6xul-5 4ojf-d 4ygv-2 3lrs-4 6cdp-d 6tcr-d 6e65-d 6mfj-1 4r7d-1 5fgb-2 6cdm-2 3uyr-d 4jo2-2 4kaq-d 6vsr-d 6axp-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

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

A: MONOCLONAL ANTIBODY F-22-30

B: MONOCLONAL ANTIBODY F-22-30

M: MONOCLONAL ANTIBODY F-22-30

N: MONOCLONAL ANTIBODY F-22-30

V: MONOCLONAL ANTIBODY F-22-30

W: MONOCLONAL ANTIBODY F-22-30

X: MONOCLONAL ANTIBODY F-22-30

Y: MONOCLONAL ANTIBODY F-22-30

191 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: MONOCLONAL ANTIBODY F-22-30

B: MONOCLONAL ANTIBODY F-22-30

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

2

M: MONOCLONAL ANTIBODY F-22-30

N: MONOCLONAL ANTIBODY F-22-30

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

3

V: MONOCLONAL ANTIBODY F-22-30

W: MONOCLONAL ANTIBODY F-22-30

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

4

X: MONOCLONAL ANTIBODY F-22-30

Y: MONOCLONAL ANTIBODY F-22-30

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

Unit cell

Length a, b, c (Å)	75.060, 75.225, 98.409
Angle α, β, γ (deg.)	111.05, 90.39, 106.83
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	M
3	1	V
4	1	X
1	2	B
2	2	N
3	2	W
4	2	Y

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	3	A	1 - 217
2	1	1	3	M	1 - 217
3	1	1	3	V	1 - 217
4	1	1	3	X	1 - 217
1	1	2	3	B	1 - 220
2	1	2	3	N	1 - 220
3	1	2	3	W	1 - 220
4	1	2	3	Y	1 - 220

NCS ensembles :

ID
1
2

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.29114, -0.95668, 0.00301), (-0.95667, -0.29115, -0.00408), (0.00478, -0.0017, -1)	9.47417, 49.05562, -44.67607
2	given	(-0.99989, 0.00116, -0.01478), (-0.0014, -0.99987, 0.01587), (-0.01476, 0.01589, 0.99976)	-35.50264, 1.89914, 0.29001
3	given	(-0.29091, 0.95675, -0.00211), (0.95654, 0.29089, 0.02037), (0.0201, 0.0039, -0.99979)	19.42807, 10.69092, -45.04293

#1: Antibody	MONOCLONAL ANTIBODY F-22-30 Mass: 24175.725 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell line: F-22-30 MURIN HYBRIDOMA
#2: Antibody	MONOCLONAL ANTIBODY F-22-30 Mass: 23490.211 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell line: F-22-30 MURIN HYBRIDOMA
Sequence details	THE SEQUENCE OF THE PROTEIN WAS NOT DEPOSITED INTO ANY SEQUENCE DATABASE

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.5 Å³/Da / Density % sol: 50 % / Description: NONE
Crystal grow	pH: 5 Details: 18% (V/V) OF PEG 4000, 0.1M NA CITRATE, 0.2 M MAGNESIUM SULFATE, PH 5.0

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0052
Detector	Type: MARRESEARCH / Detector: CCD / Date: Jul 9, 2005
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0052 Å / Relative weight: 1
Reflection	Resolution: 2.5→45 Å / Num. obs: 64354 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 2 % / R_merge(I) obs: 0.05 / Net I/σ(I): 17.6
Reflection shell	Resolution: 2.5→2.64 Å / Redundancy: 2 % / R_merge(I) obs: 0.23 / Mean I/σ(I) obs: 5.7 / % possible all: 97.1

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
MOSFLM		data reduction
SCALA		data scaling
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: SET OF SEVERAL FAB STRUCTURES FROM THE WWPDB

Resolution: 2.5→91.29 Å / Cor.coef. F_o:F_c: 0.935 / Cor.coef. F_o:F_c free: 0.903 / SU B: 22.683 / SU ML: 0.225 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.657 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.257	3275	5.1 %	RANDOM
R_work	0.211	-	-	-
obs	0.213	61078	97.5 %	-

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: 33.15 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.11 Å²	1.36 Å²	-0.39 Å²
2-	-	0.31 Å²	-1 Å²
3-	-	-	-0.35 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→91.29 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13057	0	0	0	13057

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.022	13393
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.965	1.95	18273
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.133	5	1706
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.869	24.574	516
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.529	15	2105
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	23.237	15	46
X-RAY DIFFRACTION	r_chiral_restr	0.127	0.2	2074
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	10078
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.229	0.2	5260
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.316	0.2	9013
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.144	0.2	399
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	0.317	0.2	45
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.317	0.2	4
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	0.676	1.5	8759
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.174	2	13928
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.271	3	5390
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	3.395	4.5	4345
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	864	tight positional	0.07	0.05
1	2	M	864	tight positional	0.06	0.05
1	3	V	864	tight positional	0.08	0.05
1	4	X	864	tight positional	0.06	0.05
2	1	B	852	tight positional	0.07	0.05
2	2	N	852	tight positional	0.07	0.05
2	3	W	852	tight positional	0.07	0.05
2	4	Y	852	tight positional	0.06	0.05
1	1	A	795	loose positional	0.42	5
1	2	M	795	loose positional	0.39	5
1	3	V	795	loose positional	0.41	5
1	4	X	795	loose positional	0.48	5
2	1	B	744	loose positional	0.32	5
2	2	N	744	loose positional	0.32	5
2	3	W	744	loose positional	0.37	5
2	4	Y	744	loose positional	0.34	5
1	1	A	864	tight thermal	0.14	0.5
1	2	M	864	tight thermal	0.14	0.5
1	3	V	864	tight thermal	0.14	0.5
1	4	X	864	tight thermal	0.12	0.5
2	1	B	852	tight thermal	0.16	0.5
2	2	N	852	tight thermal	0.17	0.5
2	3	W	852	tight thermal	0.16	0.5
2	4	Y	852	tight thermal	0.15	0.5
1	1	A	795	loose thermal	1.75	10
1	2	M	795	loose thermal	1.86	10
1	3	V	795	loose thermal	1.78	10
1	4	X	795	loose thermal	1.93	10
2	1	B	744	loose thermal	1.65	10
2	2	N	744	loose thermal	1.69	10
2	3	W	744	loose thermal	1.74	10
2	4	Y	744	loose thermal	1.59	10

LS refinement shell

Resolution: 2.5→2.56 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.37	245
R_work	0.305	4464

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	1.612	-0.1969	0.4259	1.9227	-0.9072	3.3542	-0.0794	0.0386	-0.4139	0.3161	0.0698	-0.1027	0.1157	0.2393	0.0096	-0.2429	-0.0226	0.0181	-0.113	-0.0711	-0.0879	0.588	-15.1205	0.6365
2	2.2425	0.7491	0.2716	2.7462	1.1255	4.2791	-0.0869	-0.1034	0.5191	0.0387	0.0149	0.0248	-0.5103	-0.4411	0.072	-0.2422	0.0478	-0.0231	-0.0891	-0.0232	-0.1087	-0.6033	18.5939	-1.8341
3	1.8707	0.1947	-0.9182	1.1987	0.4721	4.0992	-0.0012	0.2872	-0.0918	-0.0103	-0.0272	-0.2946	0.2424	0.3091	0.0285	-0.1167	0.0386	-0.0125	-0.2151	-0.0091	-0.1735	24.1368	52.9013	-45.3037
4	2.222	1.1625	0.4214	2.8117	1.0299	4.9683	0.0427	0.018	-0.0888	-0.0467	-0.1111	0.398	-0.1348	-0.6785	0.0684	-0.1068	0.0721	-0.0019	-0.2017	-0.0214	-0.1186	-8.2774	44.3155	-42.8806
5	2.157	-0.5345	-0.5891	1.8699	0.9532	3.9657	-0.1462	-0.2127	0.5871	0.3367	0.0475	-0.0725	-0.1421	-0.2916	0.0987	-0.2394	-0.0259	-0.0611	0.0086	-0.076	-0.0097	-36.1587	16.9681	0.7259
6	2.7913	0.5803	-0.4379	2.6853	-0.9133	4.3804	-0.0302	-0.311	-0.6495	0.186	-0.0742	-0.1085	0.5416	0.5379	0.1043	-0.2045	0.0449	0.0371	-0.009	0.047	-0.1073	-34.787	-16.4176	-1.1201
7	2.0346	-0.7328	0.8286	2.6269	-0.1187	3.5909	0.0006	0.5279	-0.278	-0.2278	-0.0712	0.777	-0.3283	-0.1881	0.0706	0.047	0.048	0.0118	-0.1724	-0.0201	0.0824	4.8003	6.9386	-45.8276
8	2.3325	0.4903	-0.9223	4.1266	-0.9919	4.4791	-0.0063	0.1533	0.157	-0.2493	-0.1455	-0.6953	0.3073	0.5863	0.1518	0.0019	0.0803	0.0487	-0.148	0.1012	-0.0315	37.1509	15.3453	-43.239

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 114
2	X-RAY DIFFRACTION	1	B	1 - 120
3	X-RAY DIFFRACTION	2	A	115 - 219
4	X-RAY DIFFRACTION	2	B	121 - 221
5	X-RAY DIFFRACTION	3	M	1 - 114
6	X-RAY DIFFRACTION	3	N	1 - 120
7	X-RAY DIFFRACTION	4	M	115 - 219
8	X-RAY DIFFRACTION	4	N	121 - 221
9	X-RAY DIFFRACTION	5	V	1 - 114
10	X-RAY DIFFRACTION	5	W	1 - 120
11	X-RAY DIFFRACTION	6	V	115 - 219
12	X-RAY DIFFRACTION	6	W	121 - 221
13	X-RAY DIFFRACTION	7	X	1 - 114
14	X-RAY DIFFRACTION	7	Y	1 - 120
15	X-RAY DIFFRACTION	8	X	115 - 219
16	X-RAY DIFFRACTION	8	Y	121 - 221

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