PDB-2vq1: anti trimeric Lewis X Fab54-5C10-A

ID or keywords:

Entry

Database: PDB / ID: 2vq1

Title

anti trimeric Lewis X Fab54-5C10-A

Components

ANTI-HUMAN FC GAMMA RECEPTOR III 3G8 GAMMA HEAVY CHAIN VARIABLE REGION
IGKV1-117 PROTEIN

Keywords

IMMUNE SYSTEM / MONOCLONAL ANTIBODY / RECEPTOR / DIAGNOSIS / SCHISTOSOMIASIS / CARBOHYDRATE RECOGNITION

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / AZIDE ION / GLYCINE

Function and homology information

Biological species

MUS MUSCULUS (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

de Geus, D.C. / van Roon, A.M.M. / Thomassen, E.A.J. / Hokke, C.H. / Deelder, A.M. / Abrahams, J.P.

Citation

Journal: Proteins / Year: 2009
Title: Characterization of a Diagnostic Fab Fragment Binding Trimeric Lewis X.
Authors: De Geus, D.C. / Van Roon, A.M.M. / Thomassen, E.A.J. / Hokke, C.H. / Deelder, A.M. / Abrahams, J.P.

History

Deposition	Mar 10, 2008	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 27, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jun 23, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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	2vq1.cif.gz	345.9 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	2vq1_validation.pdf.gz	494.8 KB	Display	wwPDB validaton report
Full document	2vq1_full_validation.pdf.gz	521.2 KB	Display
Data in XML	2vq1_validation.xml.gz	37.5 KB	Display
Data in CIF	2vq1_validation.cif.gz	51.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vq/2vq1 ftp://data.pdbj.org/pub/pdb/validation_reports/vq/2vq1	HTTPS FTP

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Related structure data

Related structure data	1uz6S S: Starting model for refinement
Similar structure data	1bey-d 1ub6-1 4nry-1 4j1u-3 6dca-4 6dca-1 1mie-d 6nv0-1 1m7i-d 4jzo-1 5t78-2 4odu-2 5mu0-8 4r7n-6 6wgk-3 6wgj-2 6ele-1 5i1d-2 5w24-d 6mh2-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

Related structure data

1uz6S

S: Starting model for refinement

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) #235 - Jul 2019 AMPA Receptor similarity (1) #142 - Oct 2011 PDB Pioneers similarity (1)

Deposited unit

A: IGKV1-117 PROTEIN

B: ANTI-HUMAN FC GAMMA RECEPTOR III 3G8 GAMMA HEAVY CHAIN VARIABLE REGION

E: IGKV1-117 PROTEIN

F: ANTI-HUMAN FC GAMMA RECEPTOR III 3G8 GAMMA HEAVY CHAIN VARIABLE REGION

hetero molecules

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

1

A: IGKV1-117 PROTEIN

B: ANTI-HUMAN FC GAMMA RECEPTOR III 3G8 GAMMA HEAVY CHAIN VARIABLE REGION

hetero molecules

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

2

E: IGKV1-117 PROTEIN

F: ANTI-HUMAN FC GAMMA RECEPTOR III 3G8 GAMMA HEAVY CHAIN VARIABLE REGION

hetero molecules

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

Unit cell

Length a, b, c (Å)	51.384, 161.015, 53.480
Angle α, β, γ (deg.)	90.00, 103.07, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Antibody / Protein , 2 types, 4 molecules AEBF

#1: Antibody	IGKV1-117 PROTEIN / FAB54-5C10-A Mass: 23960.605 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ANTIGEN BINDING FRAGMENT / Source: (natural) MUS MUSCULUS (house mouse) / Cell line: MURINE HYBRIDOMA / Strain: SWISS
#2: Protein	ANTI-HUMAN FC GAMMA RECEPTOR III 3G8 GAMMA HEAVY CHAIN VARIABLE REGION / FAB54-5C10-A Mass: 23430.354 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ANTIGEN BINDING FRAGMENT / Source: (natural) MUS MUSCULUS (house mouse) / Cell line: MURINE HYBRIDOMA / Strain: SWISS

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Non-polymers , 4 types, 226 molecules

#3: Chemical	ChemComp-GLY / GLYCINE Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₅NO₂
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-AZI / AZIDE ION Mass: 42.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: N₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.2 Å³/Da / Density % sol: 42.7 % / Description: NONE
Crystal grow	pH: 4 / Details: 0.1 M NA CITRATE PH 4, 11% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372
Detector	Type: MARRESEARCH / Detector: CCD / Date: May 6, 2005
Radiation	Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.95372 Å / Relative weight: 1
Reflection	Resolution: 2.5→28.7 Å / Num. obs: 29262 / % possible obs: 99.9 % / Observed criterion σ(I): 5 / Redundancy: 3.7 % / R_merge(I) obs: 0.06 / Net I/σ(I): 18.5
Reflection shell	Resolution: 2.5→2.64 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.24 / Mean I/σ(I) obs: 5.2 / % possible all: 100

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UZ6

1uz6

Resolution: 2.5→25 Å / Cor.coef. F_o:F_c: 0.935 / Cor.coef. F_o:F_c free: 0.882 / SU B: 22.761 / SU ML: 0.258 / Cross valid method: THROUGHOUT / ESU R Free: 0.329 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 127-133 IN CHAIN F AND 129-133 IN CHAIN B ARE DISORDERED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26	1470	5 %	RANDOM
R_work	0.203	-	-	-
obs	0.206	27751	100 %	-

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: 42.92 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.02 Å²	0 Å²	-0.59 Å²
2-	-	1.25 Å²	0 Å²
3-	-	-	0.5 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6581	0	61	214	6856

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.022	6817
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.668	1.955	9279
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	29.078	5	856
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.978	23.977	259
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.789	15	1086
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.6	15	28
X-RAY DIFFRACTION	r_chiral_restr	0.377	0.2	1048
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	5102
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.22	0.2	2861
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.304	0.2	4463
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.157	0.2	366
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	0.174	0.2	75
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.219	0.2	11
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	4.175	1.5	4305
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	6.19	2	6990
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	3.582	3	2512
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	5.449	4.5	2286
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

LS refinement shell

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

	R_factor	Num. reflection
R_free	0.361	102
R_work	0.28	2092

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	0.1615	-0.0374	-0.0128	0.0105	0.0144	0.0718	-0.0074	-0.0421	0.006	0.0068	0.0112	0.04	-0.0148	-0.0359	-0.0038	-0.0253	0.0016	-0.0055	0.0163	0.0012	0.0238	-4.2351	9.7091	13.728
2	0.0733	0.1096	-0.0338	0.4865	-0.1788	0.0666	0.0579	-0.015	-0.0183	-0.0093	-0.0443	-0.0584	0.0523	-0.02	-0.0136	-0.0251	0.0012	-0.0105	0.0221	-0.0008	0.0276	-9.2958	20.0305	-2.2896
3	0.6094	-0.5101	0.1981	0.427	-0.1658	0.0644	-0.0188	-0.0149	-0.0192	0.0521	0.0007	-0.0171	0.0025	-0.021	0.0181	-0.0204	-0.0003	-0.0091	0.0078	0.0047	0.013	-1.3192	4.2521	2.2454
4	0.1057	0.1906	0.0091	0.3436	0.0164	0.0008	0.0399	0.0035	-0.0398	0.0032	-0.0563	0.0436	0.0032	0.0103	0.0163	-0.0153	0.0009	-0.0074	0.0233	-0.0033	0.0188	-10.3467	1.0097	1.7471
5	0.1932	-0.0468	0.2028	0.0134	-0.0637	0.3176	-0.0023	0.0024	-0.044	-0.0074	-0.0064	0.0058	0.0086	0.0028	0.0087	-0.0227	0.0015	-0.0034	-0.0067	0.0062	0.0324	-6.9187	5.1635	9.4136
6	1.5568	-0.1395	-0.5108	0.0125	0.0458	0.1676	0.033	-0.0868	0.0395	-0.1538	-0.0583	0.009	-0.0956	-0.0128	0.0253	-0.0226	-0.0149	-0.0148	0.0039	0.0082	0.0139	-0.6296	17.8772	-3.7452
7	0.1062	-0.0844	0.0234	0.1372	-0.0998	0.1565	-0.0184	-0.0094	0.0011	0.027	0.0073	-0.0022	-0.0118	0.0033	0.0112	-0.0275	-0.0015	-0.0055	0.0114	-0.0018	0.0155	19.9313	-7.792	26.0505
8	1.6378	-1.0816	0.8659	1.1361	-0.2459	0.7097	-0.1199	-0.0218	0.1037	0.0588	0.1514	0.0087	0.0305	-0.0516	-0.0314	-0.0199	-0.0084	-0.0236	-0.0033	-0.0107	0.0149	35.0148	44.8223	23.0409
9	0.1029	-0.1389	-0.1346	0.3086	0.3752	0.4854	-0.0384	0.0334	0.0163	-0.0007	0.0139	0.0295	-0.03	-0.0027	0.0244	-0.0244	0.0039	-0.0073	0.0144	-0.0052	0.0259	39.9616	30.806	35.9319
10	0.7209	-0.222	0.1906	0.0684	-0.0587	0.0504	0.0052	-0.0066	-0.0463	-0.0118	0.0273	0.0345	-0.0035	-0.0302	-0.0324	-0.0159	0.0014	-0.0096	-0.0006	-0.0021	0.0151	31.8519	32.5736	19.7274
11	0.1797	0.3167	0.2192	0.5579	0.3899	0.7763	-0.013	0.0403	0.0231	-0.0051	0.0668	0.0051	0.0095	-0.0512	-0.0537	-0.036	0.0055	-0.0071	0.0101	0.0016	0.0173	40.8839	31.3968	16.4721
12	0.2346	-0.0929	-0.0538	0.1397	0.1156	0.0988	0.0176	0.0179	0.0124	-0.0005	-0.0036	-0.0024	-0.0268	-0.0363	-0.014	-0.0188	-0.0022	-0.0053	0.0211	0.0021	0.0207	37.5112	39.813	19.2843
13	0.3222	0.0727	0.0019	0.0164	0.0004	0	0.0243	-0.108	-0.0509	0.0412	0.0778	0.0748	0.0106	0.1137	-0.1022	-0.0121	0.0117	-0.0058	0.0129	0.0065	0.0139	31.2939	29.1366	34.2119
14	0.0057	0.0113	-0.0155	0.0221	-0.0305	0.0419	-0.0049	0.003	-0.0049	0.0154	0.0096	-0.003	-0.001	0.0014	-0.0047	-0.0202	0.0003	-0.0115	0.0204	-0.004	0.0129	10.7541	54.2933	4.1799
15	0.0029	-0.0031	0.0011	0.0033	-0.0011	0.0004	0.0366	-0.0133	0.0386	0.0404	-0.0231	0.0295	0.0146	-0.0059	-0.0134	-0.0144	-0.0064	-0.0106	0.0121	-0.0066	0.0198	17.5158	4.3567	-8.0328
16	2.7796	1.8208	1.2283	1.1928	0.8046	0.5428	-0.0458	-0.2808	-0.158	-0.1073	0.0264	-0.1684	-0.3273	-0.0931	0.0194	-0.0412	-0.0036	0.0035	0.0183	-0.0003	0.0139	2.1498	4.4526	-16.8805
17	0.3835	-0.1392	-0.1046	0.0536	0.0777	0.5447	-0.0342	-0.0112	-0.0834	0.0199	-0.0093	-0.0308	-0.0021	-0.0048	0.0435	-0.0153	-0.0072	-0.0095	0.0112	0.0042	0.0172	10.7338	12.2239	0.14
18	0.0466	0.2992	0.0837	1.9229	0.5377	0.1504	0.0309	-0.0772	-0.198	-0.0352	-0.1159	-0.16	-0.1144	-0.0367	0.085	-0.0304	0.014	0.0033	0.0109	-0.0038	-0.0002	3.9784	13.8426	-17.0194
19	0.0897	-0.0354	0.0074	0.014	-0.0029	0.0006	0.0149	-0.0036	0.0038	-0.0047	-0.0127	0.0119	-0.0125	0.0149	-0.0022	-0.0134	-0.0002	-0.0129	0.0155	-0.0025	0.0192	15.3797	12.6404	-9.2605
20	1.2703	-1.2472	0.5455	1.2922	-0.5054	0.2477	-0.3132	-0.3354	-0.1948	0.4629	0.0397	0.0264	0.09	0.1041	0.2734	-0.0348	-0.0266	0.0581	0.0211	-0.004	0.0263	0.0198	6.2465	-9.3228
21	0.024	-0.0354	-0.0604	0.052	0.0889	0.1518	-0.009	-0.0109	0.0284	0.0023	0.0204	0.0431	0.0355	0.0106	-0.0114	-0.0163	-0.0006	-0.0104	0.0009	0.0062	0.02	21.0189	-9.2565	8.6093
22	0.2049	-0.0093	0.0436	0.1431	-0.244	0.4198	0.0605	-0.0041	-0.0605	-0.0656	-0.0366	0.096	-0.0766	0.0351	-0.0239	0.0012	-0.0053	-0.0033	-0.0006	-0.008	0.0178	13.0339	22.3674	21.7307
23	0.5294	0.0458	-0.2216	0.7231	0.3676	1.2875	0.0164	-0.0253	-0.047	-0.1151	0.0477	-0.0288	0.0639	0.062	-0.0641	-0.0286	0.018	0.0046	0.0057	0.0019	0.0136	28.4403	13.8119	23.6879
24	0.5097	-0.2288	-0.0604	1.5132	-0.8312	0.5295	-0.0295	-0.0139	0.0442	0.0443	0.0178	-0.0037	-0.0313	0.0138	0.0117	-0.0244	0.0009	-0.0092	0.0018	0.0001	0.0192	19.8634	31.9501	27.8103
25	0.4378	0.1157	0.6311	0.0306	0.1668	0.9097	0.0136	0.0418	-0.096	0.1742	0.0722	-0.0771	-0.083	-0.0971	-0.0858	-0.0185	-0.0209	-0.0084	0.0142	0.0269	0.0405	26.7551	15.6049	33.0312
26	0.3585	-0.1791	-0.0141	0.0975	-0.0245	0.123	-0.0055	-0.0037	-0.0385	0.0139	-0.0003	0.0839	-0.0301	0.0012	0.0058	-0.0115	-0.0006	-0.0044	0.0106	0.0026	0.0163	15.3115	22.9617	30.1924
27	7.3673	0.3602	1.0128	0.2531	0.2855	0.3757	0.0001	-0.0881	0.1251	-0.0626	0.0353	0.0017	0.05	-0.0329	-0.0354	-0.0162	0.0038	0.0007	-0.0025	0.0166	-0.003	30.5461	21.4908	23.9313
28	0.0029	-0.014	-0.0072	0.0675	0.0346	0.0177	-0.0079	0.0285	-0.0281	-0.0144	-0.0007	0.0136	-0.007	-0.0155	0.0086	-0.0223	0.0071	-0.012	0.031	0.0012	0.0235	9.5211	36.9048	5.1058

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	E	1 - 23
2	X-RAY DIFFRACTION	2	E	24 - 36
3	X-RAY DIFFRACTION	3	E	37 - 54
4	X-RAY DIFFRACTION	4	E	55 - 68
5	X-RAY DIFFRACTION	5	E	69 - 93
6	X-RAY DIFFRACTION	6	E	94 - 102
7	X-RAY DIFFRACTION	7	E	103 - 216
8	X-RAY DIFFRACTION	8	A	1 - 23
9	X-RAY DIFFRACTION	9	A	24 - 36
10	X-RAY DIFFRACTION	10	A	37 - 54
11	X-RAY DIFFRACTION	11	A	55 - 68
12	X-RAY DIFFRACTION	12	A	69 - 93
13	X-RAY DIFFRACTION	13	A	94 - 102
14	X-RAY DIFFRACTION	14	A	103 - 216
15	X-RAY DIFFRACTION	15	F	1 - 25
16	X-RAY DIFFRACTION	16	F	26 - 37
17	X-RAY DIFFRACTION	17	F	38 - 51
18	X-RAY DIFFRACTION	18	F	52 - 60
19	X-RAY DIFFRACTION	19	F	61 - 96
20	X-RAY DIFFRACTION	20	F	97 - 103
21	X-RAY DIFFRACTION	21	F	104 - 215
22	X-RAY DIFFRACTION	22	B	1 - 25
23	X-RAY DIFFRACTION	23	B	26 - 37
24	X-RAY DIFFRACTION	24	B	38 - 51
25	X-RAY DIFFRACTION	25	B	52 - 60
26	X-RAY DIFFRACTION	26	B	61 - 96
27	X-RAY DIFFRACTION	27	B	97 - 103
28	X-RAY DIFFRACTION	28	B	104 - 215

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