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- PDB-5uff: Crystal Structure of Variable Lymphocyte Receptor (VLR) RBC36 wit... -

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Basic information

Entry
Database: PDB / ID: 5uff
TitleCrystal Structure of Variable Lymphocyte Receptor (VLR) RBC36 with Fucose(alpha-1-2)Lactose bound
ComponentsRBC36
KeywordsIMMUNE SYSTEM / variable lymphocyte receptors / VLR / leucine-rich repeat / LRR / adaptive immunity / sea lamprey / jawless fish / receptor / glycan binding / glycan receptor
Function / homology2'-fucosyllactose
Function and homology information
Biological speciesPetromyzon marinus (sea lamprey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.137 Å
AuthorsCollins, B.C. / Gunn, R.J. / McKitrick, T.R. / Herrin, B.R. / Cummings, R.D. / Cooper, M.D. / 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.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: RBC36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2522
Polymers23,7631
Non-polymers4881
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.969, 47.503, 57.276
Angle α, β, γ (deg.)90.000, 85.690, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RBC36


Mass: 23763.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Petromyzon marinus (sea lamprey) / Production host: Spodoptera frugiperda (fall armyworm)
#2: Polysaccharide alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / 2'-fucosyllactose


Type: oligosaccharide, Oligosaccharide / Class: Glycan component / Mass: 488.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 2'-fucosyllactose
DescriptorTypeProgram
LFucpa1-2DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5][a2112h-1b_1-5][a1221m-1a_1-5]/1-2-3/a4-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.28 Å3/Da / Density % sol: 46.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 11.4 mg/mL RBC36, 6.9 mM fucose(alpha-1-2)lactose, 140 mM ammonium chloride, 22% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9784 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 5, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9784 Å / Relative weight: 1
ReflectionResolution: 2.137→39.865 Å / Num. obs: 11758 / % possible obs: 97 % / Redundancy: 6.5 % / Rpim(I) all: 0.07 / Net I/σ(I): 8
Reflection shellResolution: 2.137→2.21 Å / Num. measured obs: 7003 / Num. unique all: 1106 / Rpim(I) all: 0.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3E6J

3e6j


Resolution: 2.137→39.856 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 39.58
RfactorNum. reflection% reflection
Rfree0.2824 560 4.8 %
Rwork0.2231 --
obs0.2259 11655 96.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 83.69 Å2 / Biso mean: 37.6366 Å2 / Biso min: 21.08 Å2
Refinement stepCycle: final / Resolution: 2.137→39.856 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1619 0 33 61 1713
Biso mean--38.98 39.11 -
Num. residues----216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071694
X-RAY DIFFRACTIONf_angle_d1.1172312
X-RAY DIFFRACTIONf_chiral_restr0.04271
X-RAY DIFFRACTIONf_plane_restr0.005290
X-RAY DIFFRACTIONf_dihedral_angle_d27.879656
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1371-2.35210.43841400.37032674281494
2.3521-2.69240.37011490.2742756290597
2.6924-3.39190.2741450.23272813295898
3.3919-39.86310.22251260.17482852297898

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