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- PDB-5uei: Crystal Structure of Variable Lymphocyte Receptor (VLR) O13 (Apo) -

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Basic information

Entry
Database: PDB / ID: 5uei
TitleCrystal Structure of Variable Lymphocyte Receptor (VLR) O13 (Apo)
ComponentsO13
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 / Resolution: 1.702 Å
AuthorsGunn, R.J. / Collins, B.C. / McKitrick, T.R. / Cummings, R.D. / Herrin, B.R. / 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 2, 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 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: O13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6794
Polymers27,4591
Non-polymers2203
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint-9 kcal/mol
Surface area11560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.663, 86.663, 38.108
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein O13


Mass: 27459.350 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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.65 Å3/Da / Density % sol: 53.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 22% PEG4000, 0.14 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 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: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 31376 / % possible obs: 99.9 % / Redundancy: 10.9 % / Biso Wilson estimate: 26.86 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 6.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured obsNum. unique allCC1/2% possible all
1.7-1.7310.90.9231798915730.824100
1.73-1.7610.70.7390.888100
1.76-1.7910.40.6620.88599.9
1.79-1.83100.530.91898.8
1.83-1.8711.30.430.955100
1.87-1.9111.20.3440.966100
1.91-1.9611.20.2740.977100
1.96-2.0211.10.2320.983100
2.02-2.0710.90.1970.986100
2.07-2.1410.60.1710.9999.7
2.14-2.2210.10.1490.9999.8
2.22-2.3111.40.1360.995100
2.31-2.4111.30.1230.993100
2.41-2.5411.20.110.995100
2.54-2.7110.0980.996100
2.7-2.9110.30.0880.99699.8
2.91-3.211.60.0810.997100
3.2-3.6611.30.0720.997100
3.66-4.6110.50.0650.99799.9
4.61-5010.60.0650.99799.9

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Processing

Software
NameVersionClassification
DENZOdata collection
SCALEPACKdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
DENZOdata reduction
MOLREPphasing
RefinementResolution: 1.702→43.331 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.43
RfactorNum. reflection% reflection
Rfree0.1846 1524 4.86 %
Rwork0.1585 --
obs0.1598 31361 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 95.84 Å2 / Biso mean: 33.5809 Å2 / Biso min: 16.7 Å2
Refinement stepCycle: final / Resolution: 1.702→43.331 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1883 0 13 278 2174
Biso mean--42.28 43.78 -
Num. residues----246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121942
X-RAY DIFFRACTIONf_angle_d1.32641
X-RAY DIFFRACTIONf_chiral_restr0.066313
X-RAY DIFFRACTIONf_plane_restr0.006340
X-RAY DIFFRACTIONf_dihedral_angle_d13.403707
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7022-1.75710.26661570.22512647280499
1.7571-1.81990.23031670.19772665283299
1.8199-1.89280.22121320.180427072839100
1.8928-1.97890.20051480.158626662814100
1.9789-2.08330.20961200.157927072827100
2.0833-2.21380.18511220.149827222844100
2.2138-2.38470.20241260.154827152841100
2.3847-2.62470.18051230.160827412864100
2.6247-3.00440.22251420.174226952837100
3.0044-3.78490.17421500.15427572907100
3.7849-43.34550.15171370.147528152952100
Refinement TLS params.Method: refined / Origin x: 28.0418 Å / Origin y: 18.1227 Å / Origin z: 4.5571 Å
111213212223313233
T0.1529 Å20.0026 Å2-0.0225 Å2-0.188 Å2-0.0153 Å2--0.1667 Å2
L0.8849 °2-0.8661 °2-0.0332 °2-2.4478 °20.2377 °2--0.6057 °2
S0.0306 Å °-0.0257 Å °-0.0377 Å °-0.0924 Å °-0.0901 Å °0.3004 Å °0.0304 Å °-0.0548 Å °0.0428 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA17 - 262
2X-RAY DIFFRACTION1allB1
3X-RAY DIFFRACTION1allC1 - 2
4X-RAY DIFFRACTION1allS1 - 293

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