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- PDB-5ufb: Crystal Structure of Variable Lymphocyte Receptor (VLR) Tn4-22 (Apo) -

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Basic information

Entry
Database: PDB / ID: 5ufb
TitleCrystal Structure of Variable Lymphocyte Receptor (VLR) Tn4-22 (Apo)
ComponentsTn4-22
KeywordsIMMUNE SYSTEM / variable lymphocyte receptors / VLR / leucine-rich repeat / LRR / adaptive immunity / sea lamprey / jawless fish / receptor / glycan binding / glycan receptor
Biological speciesPetromyzon marinus (sea lamprey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.844 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 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tn4-22


Theoretical massNumber of molelcules
Total (without water)27,7191
Polymers27,7191
Non-polymers00
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.688, 83.688, 115.073
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Tn4-22


Mass: 27718.572 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Petromyzon marinus (sea lamprey) / Production host: Homo sapiens (human)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 3.75 Å3/Da / Density % sol: 67.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 21.6 mg/mL Tn4-22, 100 mM sodium acetate, pH 4.6, 200 mM lithium sulfate, 2.7 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 16, 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: 1.844→41.844 Å / Num. obs: 33959 / % possible obs: 100 % / Redundancy: 6.6 % / Rpim(I) all: 0.03 / Net I/σ(I): 15.1
Reflection shellResolution: 1.844→1.91 Å / Num. unique all: 20103 / Rpim(I) all: 0.41

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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: 1.844→41.844 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.84
RfactorNum. reflection% reflection
Rfree0.2131 1762 5.19 %
Rwork0.2064 --
obs0.2068 33934 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.19 Å2 / Biso mean: 40.5862 Å2 / Biso min: 24.95 Å2
Refinement stepCycle: final / Resolution: 1.844→41.844 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1823 0 0 92 1915
Biso mean---42.45 -
Num. residues----241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071865
X-RAY DIFFRACTIONf_angle_d1.0242543
X-RAY DIFFRACTIONf_chiral_restr0.042305
X-RAY DIFFRACTIONf_plane_restr0.004329
X-RAY DIFFRACTIONf_dihedral_angle_d13.217662
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8439-1.89380.4685970.4062453255098
1.8938-1.94950.32781390.28092452259199
1.9495-2.01240.25271280.259124902618100
2.0124-2.08440.30761530.231624372590100
2.0844-2.16780.2681570.234724722629100
2.1678-2.26650.28611160.238624762592100
2.2665-2.3860.24761600.228824322592100
2.386-2.53540.2495770.243225622639100
2.5354-2.73110.25461270.240524692596100
2.7311-3.00590.24931270.24824952622100
3.0059-3.44070.24721350.228925052640100
3.4407-4.33420.18392050.166324152620100
4.3342-41.85480.14771410.153825142655100

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