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

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Basic information

Entry
Database: PDB / ID: 6ev2
TitleCrystal structure of antibody against schizophyllan in complex with laminarihexaose
Components
  • Heavy chain
  • Light chain
KeywordsIMMUNE SYSTEM / Antibody / Fab / Schizophyllan / laminarihexaose
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / beta-laminaribiose / beta-D-glucopyranose
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.403 Å
AuthorsSung, K.H. / Josewski, J. / Duebel, S. / Blankenfeldt, W. / Rau, U.
CitationJournal: 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
DepositionNov 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: 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 2.1Jan 17, 2024Group: 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
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)189,34510
Polymers188,8228
Non-polymers5222
Water9,530529
1
A: Heavy chain
B: Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3863
Polymers47,2062
Non-polymers1801
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-24 kcal/mol
Surface area19530 Å2
MethodPISA
2
C: Heavy chain
D: Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5483
Polymers47,2062
Non-polymers3421
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-23 kcal/mol
Surface area19350 Å2
MethodPISA
3
E: Heavy chain
F: Light chain


Theoretical massNumber of molelcules
Total (without water)47,2062
Polymers47,2062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-26 kcal/mol
Surface area19830 Å2
MethodPISA
4
G: Heavy chain
H: Light chain


Theoretical massNumber of molelcules
Total (without water)47,2062
Polymers47,2062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-26 kcal/mol
Surface area19830 Å2
MethodPISA
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 number4
Space group name H-MP1211

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Components

#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
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#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
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 529 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 52.51 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.4→91 Å / Num. obs: 74793 / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.039 / Rrim(I) all: 0.103 / Net I/σ(I): 12.9
Reflection shellResolution: 2.403→2.445 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.779 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3694 / Rpim(I) all: 0.312 / Rrim(I) all: 0.84 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.2329 3664 4.91 %
Rwork0.1935 --
obs0.1954 74686 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.403→55.787 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13102 0 35 529 13666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413486
X-RAY DIFFRACTIONf_angle_d0.75618369
X-RAY DIFFRACTIONf_dihedral_angle_d12.6158064
X-RAY DIFFRACTIONf_chiral_restr0.0462061
X-RAY DIFFRACTIONf_plane_restr0.0062307
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4033-2.43490.3461160.29282741X-RAY DIFFRACTION100
2.4349-2.46830.32031470.27252713X-RAY DIFFRACTION100
2.4683-2.50360.34661380.27642723X-RAY DIFFRACTION100
2.5036-2.54090.3391180.25872729X-RAY DIFFRACTION100
2.5409-2.58060.3221520.24642751X-RAY DIFFRACTION100
2.5806-2.62290.30161410.25252721X-RAY DIFFRACTION100
2.6229-2.66820.30911450.24282735X-RAY DIFFRACTION100
2.6682-2.71670.27221520.24712678X-RAY DIFFRACTION100
2.7167-2.76890.31031230.24762734X-RAY DIFFRACTION100
2.7689-2.82540.30311460.24452733X-RAY DIFFRACTION100
2.8254-2.88690.27361270.24642725X-RAY DIFFRACTION100
2.8869-2.9540.26511320.24362760X-RAY DIFFRACTION100
2.954-3.02790.2881600.2392734X-RAY DIFFRACTION100
3.0279-3.10980.25011360.2312679X-RAY DIFFRACTION100
3.1098-3.20130.27191400.2152743X-RAY DIFFRACTION100
3.2013-3.30460.27021380.20952732X-RAY DIFFRACTION100
3.3046-3.42270.22251370.20692754X-RAY DIFFRACTION100
3.4227-3.55970.19221480.2022741X-RAY DIFFRACTION100
3.5597-3.72170.23091550.19472710X-RAY DIFFRACTION100
3.7217-3.91780.21151460.18972705X-RAY DIFFRACTION100
3.9178-4.16320.23181300.16442762X-RAY DIFFRACTION100
4.1632-4.48450.20121370.14192741X-RAY DIFFRACTION100
4.4845-4.93560.16521510.13222723X-RAY DIFFRACTION100
4.9356-5.64920.18051610.14522747X-RAY DIFFRACTION100
5.6492-7.11510.20991460.1712756X-RAY DIFFRACTION100
7.1151-55.80220.20391420.16722752X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
11.81881.2917-0.1693.27890.3456-0.1660.222-0.763-0.10220.166-0.3699-0.26590.03950.11850.1450.5483-0.084-0.01160.81710.07160.29718.2188-2.846347.3859
21.88511.2844-0.1672.412-0.10610.41680.0299-0.45610.08320.0662-0.1307-0.00390.01770.15020.09230.41820.018-0.01540.4168-0.03790.194-7.3907-1.725738.8312
31.2613-1.87280.04154.8335-0.88080.10570.13350.2864-0.1521-0.2746-0.08050.30820.0155-0.1286-0.04410.51160.0283-0.04730.4637-0.0460.268631.7546-1.1243-2.4214
41.1335-1.1502-0.15022.767-0.30020.2868-0.04940.26840.03510.0501-0.00540.0418-0.0194-0.11090.07620.4374-0.041-0.04820.38120.00040.234946.9482-0.83136.632
50.87720.17920.1893.11680.36260.6037-0.06250.565-0.0118-0.42110.0815-0.29270.10590.0961-0.00230.6304-0.09540.11290.93410.03120.3581.1148-3.9494-9.4481
61.7842-0.9783-0.15762.78650.30730.6501-0.01640.4791-0.01270.0156-0.00530.01550.00130.08750.03380.3944-0.06870.01330.4509-0.01390.2069-11.9494-5.08133.5579
70.79040.4654-0.10763.764-0.87420.3487-0.0442-0.23370.04760.47250.18290.2612-0.0528-0.1215-0.11560.58890.09310.08930.5384-0.01470.263838.0921-5.995354.5355
81.38891.038-0.46943.21170.03430.4781-0.0412-0.2449-0.02140.11160.0458-0.07160.00170.03070.00950.38780.0535-0.01630.39570.02330.217751.4274-6.429641.777
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 1:220)
2X-RAY DIFFRACTION2(chain B and resseq 1:217)
3X-RAY DIFFRACTION3(chain C and resseq 1:222)
4X-RAY DIFFRACTION4(chain D and resseq 1:217)
5X-RAY DIFFRACTION5(chain E and resseq 1:220)
6X-RAY DIFFRACTION6(chain F and resseq 1:213)
7X-RAY DIFFRACTION7(chain G and resseq 1:220)
8X-RAY DIFFRACTION8(chain H and resseq 1:213)

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