PDB-6ev2: Crystal structure of antibody against schizophyllan in complex wi...

ID or keywords:

Entry

Database: PDB / ID: 6ev2

Title

Crystal structure of antibody against schizophyllan in complex with laminarihexaose

Components

Heavy chain
Light chain

Keywords

IMMUNE SYSTEM / Antibody / Fab / Schizophyllan / laminarihexaose

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / beta-laminaribiose / beta-D-glucopyranose

Function and homology information

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.403 Å

Authors

Sung, K.H. / Josewski, J. / Duebel, S. / Blankenfeldt, W. / Rau, U.

Citation

Journal: Sci Rep / Year: 2018
Title: Structural insights into antigen recognition of an anti-beta-(1,6)-beta-(1,3)-D-glucan antibody.
Authors: Sung, K.H. / Josewski, J. / Dubel, S. / Blankenfeldt, W. / Rau, U.

History

Deposition	Nov 1, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 26, 2018	Provider: repository / Type: Initial release
Revision 2.0	Jul 29, 2020	Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / software / struct_asym / struct_conn / struct_site / struct_site_gen Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1	Jan 17, 2024	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6ev2.cif.gz	669.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6ev2.ent.gz	557.9 KB	Display	PDB format
PDBx/mmJSON format	6ev2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6ev2_validation.pdf.gz	768.2 KB	Display	wwPDB validaton report
Full document	6ev2_full_validation.pdf.gz	780.6 KB	Display
Data in XML	6ev2_validation.xml.gz	63.8 KB	Display
Data in CIF	6ev2_validation.cif.gz	89.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ev/6ev2 ftp://data.pdbj.org/pub/pdb/validation_reports/ev/6ev2	HTTPS FTP

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Related structure data

Related structure data	6ev1SC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6a0x-2 35c8-d 5u4r-1 2ojz-1 2fjf-7 5hdb-4 6ugu-2 6a0x-4 6w7y-2 4nm4-2 4evn-8 3i9g-d 4uil-d 4j8r-1 6a0x-3 2a6k-1 2v7h-2 1kno-2 6me1-1 12e8-1 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

Related structure data

6ev1SC

S: Starting model for refinement

C: citing same article (ref.)

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) #198 - Jun 2016 Beta-galactosidase similarity (1) #75 - Mar 2006 Tissue Factor similarity (1) #77 - May 2006 Glucose Oxidase similarity (1)

Deposited unit

A: Heavy chain

B: Light chain

C: Heavy chain

D: Light chain

E: Heavy chain

F: Light chain

G: Heavy chain

H: Light chain

hetero molecules

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

1

A: Heavy chain

B: Light chain

hetero molecules

defined by author&software
Evidence: gel filtration
47.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Heavy chain

D: Light chain

hetero molecules

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

3

E: Heavy chain

F: Light chain

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

4

G: Heavy chain

H: Light chain

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

Unit cell

Length a, b, c (Å)	81.732, 131.502, 91.034
Angle α, β, γ (deg.)	90.00, 91.50, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Antibody

Heavy chain

Mass: 23665.475 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mus musculus (house mouse) / Production host:

Homo sapiens (human)

#2: Antibody

Light chain

Mass: 23540.115 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mus musculus (house mouse) / Production host:

Homo sapiens (human)

#3: Polysaccharide

beta-D-glucopyranose-(1-3)-beta-D-glucopyranose / beta-laminaribiose

Type: oligosaccharide, Oligosaccharide / Class: Antimicrobial / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-laminaribiose

#4: Sugar

ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose

Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C₆H₁₂O₆

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 529 / 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: 2.39 Å³/Da / Density % sol: 52.51 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: HEPES, Sodium acetate, lithium sulfate, PEG 4,000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 6, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0332 Å / Relative weight: 1
Reflection	Resolution: 2.4→91 Å / Num. obs: 74793 / % possible obs: 100 % / Redundancy: 6.9 % / R_merge(I) obs: 0.096 / R_pim(I) all: 0.039 / R_rim(I) all: 0.103 / Net I/σ(I): 12.9
Reflection shell	Resolution: 2.403→2.445 Å / Redundancy: 7.1 % / R_merge(I) obs: 0.779 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3694 / R_pim(I) all: 0.312 / R_rim(I) all: 0.84 / % possible all: 99.6

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Processing

Software

Name	Version	Classification
PHENIX	(1.12_2829: ???)	refinement
XDS		data reduction
autoPROC		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6EV1

6ev1

Resolution: 2.403→55.787 Å / SU ML: 0.31 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 26.14 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2329	3664	4.91 %
R_work	0.1935	-	-
obs	0.1954	74686	99.86 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.403→55.787 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13102	0	35	529	13666

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	13486
X-RAY DIFFRACTION	f_angle_d	0.756	18369
X-RAY DIFFRACTION	f_dihedral_angle_d	12.615	8064
X-RAY DIFFRACTION	f_chiral_restr	0.046	2061
X-RAY DIFFRACTION	f_plane_restr	0.006	2307

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 (%)
2.4033-2.4349	0.346	116	0.2928	2741	X-RAY DIFFRACTION	100
2.4349-2.4683	0.3203	147	0.2725	2713	X-RAY DIFFRACTION	100
2.4683-2.5036	0.3466	138	0.2764	2723	X-RAY DIFFRACTION	100
2.5036-2.5409	0.339	118	0.2587	2729	X-RAY DIFFRACTION	100
2.5409-2.5806	0.322	152	0.2464	2751	X-RAY DIFFRACTION	100
2.5806-2.6229	0.3016	141	0.2525	2721	X-RAY DIFFRACTION	100
2.6229-2.6682	0.3091	145	0.2428	2735	X-RAY DIFFRACTION	100
2.6682-2.7167	0.2722	152	0.2471	2678	X-RAY DIFFRACTION	100
2.7167-2.7689	0.3103	123	0.2476	2734	X-RAY DIFFRACTION	100
2.7689-2.8254	0.3031	146	0.2445	2733	X-RAY DIFFRACTION	100
2.8254-2.8869	0.2736	127	0.2464	2725	X-RAY DIFFRACTION	100
2.8869-2.954	0.2651	132	0.2436	2760	X-RAY DIFFRACTION	100
2.954-3.0279	0.288	160	0.239	2734	X-RAY DIFFRACTION	100
3.0279-3.1098	0.2501	136	0.231	2679	X-RAY DIFFRACTION	100
3.1098-3.2013	0.2719	140	0.215	2743	X-RAY DIFFRACTION	100
3.2013-3.3046	0.2702	138	0.2095	2732	X-RAY DIFFRACTION	100
3.3046-3.4227	0.2225	137	0.2069	2754	X-RAY DIFFRACTION	100
3.4227-3.5597	0.1922	148	0.202	2741	X-RAY DIFFRACTION	100
3.5597-3.7217	0.2309	155	0.1947	2710	X-RAY DIFFRACTION	100
3.7217-3.9178	0.2115	146	0.1897	2705	X-RAY DIFFRACTION	100
3.9178-4.1632	0.2318	130	0.1644	2762	X-RAY DIFFRACTION	100
4.1632-4.4845	0.2012	137	0.1419	2741	X-RAY DIFFRACTION	100
4.4845-4.9356	0.1652	151	0.1322	2723	X-RAY DIFFRACTION	100
4.9356-5.6492	0.1805	161	0.1452	2747	X-RAY DIFFRACTION	100
5.6492-7.1151	0.2099	146	0.171	2756	X-RAY DIFFRACTION	100
7.1151-55.8022	0.2039	142	0.1672	2752	X-RAY DIFFRACTION	98

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	1.8188	1.2917	-0.169	3.2789	0.3456	-0.166	0.222	-0.763	-0.1022	0.166	-0.3699	-0.2659	0.0395	0.1185	0.145	0.5483	-0.084	-0.0116	0.8171	0.0716	0.2971	8.2188	-2.8463	47.3859
2	1.8851	1.2844	-0.167	2.412	-0.1061	0.4168	0.0299	-0.4561	0.0832	0.0662	-0.1307	-0.0039	0.0177	0.1502	0.0923	0.4182	0.018	-0.0154	0.4168	-0.0379	0.194	-7.3907	-1.7257	38.8312
3	1.2613	-1.8728	0.0415	4.8335	-0.8808	0.1057	0.1335	0.2864	-0.1521	-0.2746	-0.0805	0.3082	0.0155	-0.1286	-0.0441	0.5116	0.0283	-0.0473	0.4637	-0.046	0.2686	31.7546	-1.1243	-2.4214
4	1.1335	-1.1502	-0.1502	2.767	-0.3002	0.2868	-0.0494	0.2684	0.0351	0.0501	-0.0054	0.0418	-0.0194	-0.1109	0.0762	0.4374	-0.041	-0.0482	0.3812	0.0004	0.2349	46.9482	-0.8313	6.632
5	0.8772	0.1792	0.189	3.1168	0.3626	0.6037	-0.0625	0.565	-0.0118	-0.4211	0.0815	-0.2927	0.1059	0.0961	-0.0023	0.6304	-0.0954	0.1129	0.9341	0.0312	0.358	1.1148	-3.9494	-9.4481
6	1.7842	-0.9783	-0.1576	2.7865	0.3073	0.6501	-0.0164	0.4791	-0.0127	0.0156	-0.0053	0.0155	0.0013	0.0875	0.0338	0.3944	-0.0687	0.0133	0.4509	-0.0139	0.2069	-11.9494	-5.0813	3.5579
7	0.7904	0.4654	-0.1076	3.764	-0.8742	0.3487	-0.0442	-0.2337	0.0476	0.4725	0.1829	0.2612	-0.0528	-0.1215	-0.1156	0.5889	0.0931	0.0893	0.5384	-0.0147	0.2638	38.0921	-5.9953	54.5355
8	1.3889	1.038	-0.4694	3.2117	0.0343	0.4781	-0.0412	-0.2449	-0.0214	0.1116	0.0458	-0.0716	0.0017	0.0307	0.0095	0.3878	0.0535	-0.0163	0.3957	0.0233	0.2177	51.4274	-6.4296	41.777

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resseq 1:220)
2	X-RAY DIFFRACTION	2	(chain B and resseq 1:217)
3	X-RAY DIFFRACTION	3	(chain C and resseq 1:222)
4	X-RAY DIFFRACTION	4	(chain D and resseq 1:217)
5	X-RAY DIFFRACTION	5	(chain E and resseq 1:220)
6	X-RAY DIFFRACTION	6	(chain F and resseq 1:213)
7	X-RAY DIFFRACTION	7	(chain G and resseq 1:220)
8	X-RAY DIFFRACTION	8	(chain H and resseq 1:213)

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