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- PDB-5ufc: Crystal Structure of Variable Lymphocyte Receptor (VLR) Tn4-22 wi... -

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Basic information

Entry
Database: PDB / ID: 5ufc
TitleCrystal Structure of Variable Lymphocyte Receptor (VLR) Tn4-22 with H-trisaccharide bound
ComponentsTn4-22
KeywordsIMMUNE SYSTEM / variable lymphocyte receptors / VLR / leucine-rich repeat / LRR / adaptive immunity / sea lamprey / jawless fish / receptor / glycan binding / glycan receptor
Function / homologyH type 2 antigen, beta anomer
Function and homology information
Biological speciesPetromyzon marinus (sea lamprey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.888 Å
AuthorsCollins, B.C. / Gunn, R.J. / McKitrick, T.R. / Cummings, R.D. / Cooper, M.D. / Herrin, B.R. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Structure / Year: 2017
Title: Structural Insights into VLR Fine Specificity for Blood Group Carbohydrates.
Authors: Collins, B.C. / Gunn, R.J. / McKitrick, T.R. / Cummings, R.D. / Cooper, M.D. / Herrin, B.R. / Wilson, I.A.
History
DepositionJan 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.page_first / _citation.page_last
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer 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 / struct_conn / struct_conn_type / 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_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _entity.src_method / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: 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: Tn4-22
B: Tn4-22
C: Tn4-22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,7446
Polymers83,1563
Non-polymers1,5883
Water4,810267
1
A: Tn4-22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2482
Polymers27,7191
Non-polymers5291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tn4-22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2482
Polymers27,7191
Non-polymers5291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tn4-22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2482
Polymers27,7191
Non-polymers5291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.916, 98.916, 162.875
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Tn4-22


Mass: 27718.572 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Petromyzon marinus (sea lamprey) / Production host: Homo sapiens (human)
#2: Polysaccharide alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / H type 2 antigen / beta anomer


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 529.490 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: H type 2 antigen, beta anomer
DescriptorTypeProgram
LFucpa1-2DGalpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][a1221m-1a_1-5]/1-2-3/a4-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.77 Å3/Da / Density % sol: 55.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 11 mg/mL Tn4-22, 1 mM H-trisaccharide, 85 mM sodium acetate, pH 4.6, 170 mM ammonium acetate, 15% glycerol, 25.5% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.888→49.458 Å / Num. obs: 74657 / % possible obs: 98 % / Redundancy: 9.7 % / Rpim(I) all: 0.03 / Net I/σ(I): 14.8
Reflection shellResolution: 1.888→1.96 Å / Num. measured obs: 57174 / Num. unique all: 6177 / Rpim(I) all: 0.35

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5UFB

5ufb


Resolution: 1.888→49.458 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.5
RfactorNum. reflection% reflection
Rfree0.2314 3698 5.04 %
Rwork0.1977 --
obs0.1994 73413 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 88.75 Å2 / Biso mean: 32.69 Å2 / Biso min: 17.42 Å2
Refinement stepCycle: final / Resolution: 1.888→49.458 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5559 0 108 267 5934
Biso mean--29.09 33.09 -
Num. residues----720
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085798
X-RAY DIFFRACTIONf_angle_d1.17900
X-RAY DIFFRACTIONf_chiral_restr0.044915
X-RAY DIFFRACTIONf_plane_restr0.0051005
X-RAY DIFFRACTIONf_dihedral_angle_d13.7832291
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8884-1.91320.3775740.35131565163958
1.9132-1.93940.26831460.263527412887100
1.9394-1.96710.26711280.246326742802100
1.9671-1.99650.2931430.241426532796100
1.9965-2.02770.2981410.236527332874100
2.0277-2.06090.27091570.228326782835100
2.0609-2.09650.29141530.234126932846100
2.0965-2.13460.25511490.230126532802100
2.1346-2.17570.29051640.226126842848100
2.1757-2.22010.27251390.226726992838100
2.2201-2.26830.25261520.215327272879100
2.2683-2.32110.27861410.20326832824100
2.3211-2.37910.23751240.210227222846100
2.3791-2.44350.27471410.219727342875100
2.4435-2.51540.2691400.209227172857100
2.5154-2.59660.27571610.220827062867100
2.5966-2.68940.28261390.230727012840100
2.6894-2.7970.28551590.225426992858100
2.797-2.92430.24291430.235627302873100
2.9243-3.07850.27081380.217527482886100
3.0785-3.27130.25051390.227327382877100
3.2713-3.52380.23141520.212927352887100
3.5238-3.87830.19961430.174327682911100
3.8783-4.43920.18311540.15327592913100
4.4392-5.59170.17961260.146828392965100
5.5917-49.47490.15381520.150929363088100

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