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- PDB-7la7: O6 variable lymphocyte receptor ectodomain -

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Basic information

Entry
Database: PDB / ID: 7la7
TitleO6 variable lymphocyte receptor ectodomain
Componentsvariable lymphocyte receptor O6
KeywordsIMMUNE SYSTEM / VLR / glycosylation / sulfated glycan / glycan antigen
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciesPetromyzon marinus (sea lamprey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55100728206 Å
AuthorsBernard, S.M. / 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: Commun Biol / Year: 2021
Title: Novel lamprey antibody recognizes terminal sulfated galactose epitopes on mammalian glycoproteins.
Authors: McKitrick, T.R. / Bernard, S.M. / Noll, A.J. / Collins, B.C. / Goth, C.K. / McQuillan, A.M. / Heimburg-Molinaro, J. / Herrin, B.R. / Wilson, I.A. / Cooper, M.D. / Cummings, R.D.
History
DepositionJan 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: variable lymphocyte receptor O6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1793
Polymers19,9891
Non-polymers1902
Water2,504139
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint-11 kcal/mol
Surface area9470 Å2
Unit cell
Length a, b, c (Å)52.450, 38.276, 78.690
Angle α, β, γ (deg.)90.000, 103.794, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein variable lymphocyte receptor O6


Mass: 19989.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Petromyzon marinus (sea lamprey) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.92 Å3/Da / Density % sol: 35.9 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 1.2 M NaH2PO4, 0.8 M K2HPO4, 0.1 M glycine pH 10.5, 0.2 M Li2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.55→27.1 Å / Num. obs: 125962 / % possible obs: 99.6 % / Redundancy: 5.7 % / Biso Wilson estimate: 15.1473817615 Å2 / CC1/2: 0.894 / Rpim(I) all: 0.044 / Rsym value: 0.099 / Net I/σ(I): 12.7
Reflection shellResolution: 1.55→1.61 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2093 / CC1/2: 0.533 / Rpim(I) all: 0.501 / Rsym value: 0.815

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Processing

Software
NameVersionClassification
PHENIX1.11_2567refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3G39

3g39


Resolution: 1.55100728206→27.099200658 Å / SU ML: 0.183226892809 / Cross valid method: FREE R-VALUE / σ(F): 1.38100016978 / Phase error: 20.8349931544
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.214835295174 1114 5.06709119854 %
Rwork0.173969998204 20871 -
obs0.175958079504 21985 99.1968596309 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.6445958868 Å2
Refinement stepCycle: LAST / Resolution: 1.55100728206→27.099200658 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1329 0 10 139 1478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01059788968891411
X-RAY DIFFRACTIONf_angle_d1.085555472361947
X-RAY DIFFRACTIONf_chiral_restr0.0651899230507226
X-RAY DIFFRACTIONf_plane_restr0.00718190983589248
X-RAY DIFFRACTIONf_dihedral_angle_d16.0684207607851
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.552-1.62160.300067399131210.2621574362192455X-RAY DIFFRACTION93.8433515483
1.6216-1.70710.2377738434191300.2138485902612623X-RAY DIFFRACTION99.7102499095
1.7071-1.8140.2186728646291390.1920015440392598X-RAY DIFFRACTION100
1.814-1.9540.2318567270841320.1793856646562596X-RAY DIFFRACTION100
1.954-2.15060.2102930167791470.1692179702992632X-RAY DIFFRACTION99.964028777
2.1506-2.46160.216009915531620.1678835343992604X-RAY DIFFRACTION100
2.4616-3.10070.1985993602241390.1687574901912647X-RAY DIFFRACTION100
3.1007-27.090.2059014997431440.1591913587272716X-RAY DIFFRACTION100
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)
14.222152787771.954599648190.3009106204592.58857317305-0.9619020743552.42375893730.0535666680337-0.972141255122-0.619424518602-0.0481223096617-0.263686265747-0.3826149951090.6256244427170.436428938370.2208787315810.3207714498860.03355782851210.01271401689140.3951367280720.1061119520860.21607476171310.01326534795.916972789231.190416516
22.856943800260.304201515296-0.724906381232.55443114883-0.5707182732763.41215708627-0.014817849415-0.268134666478-0.1243388191120.162722749349-0.02186407938740.05021064043540.152667122489-0.1044379365210.01913358137130.10445166132-0.00550566299694-0.000239022201850.1172710088640.006927325810840.1014140416637.334202586498.6018749340119.81301421
32.737937719550.939236410363-0.9730079989861.994511525640.01003733329324.01275853179-0.0468443132168-0.01801552617070.00606694761111-0.05628239980990.04839629030250.03081682026770.0457711561086-0.0320568570006-0.001313219814250.06553688577730.0177875416256-0.02396719558290.04435196259310.005906035344730.1110014693257.185252901516.82859588828.24891973739
41.83252727742-0.06918224946180.4092165178052.785614793550.1935243111285.012468836070.019239110348-0.2907988436340.3217776902180.167797327312-0.08309331056830.18079734674-0.471224379165-0.1448696145710.04979368643510.1418415963660.01446827473690.01430320993660.121104991492-0.06275725507420.1809509077662.6532878919225.414413372915.8136923415
52.53263864716-0.662654320152-0.8653343570631.364128048930.1458928724012.939055332150.0218410729097-0.04274642555090.0490086110336-0.1257899307550.00650537530334-0.102734743028-0.06192548614680.110183596219-0.02682730404550.139426592855-0.016740818224-0.02483509929730.08520220742010.01642659631620.15226839375712.757071284724.2951224993-0.00922282935419
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:24)
2X-RAY DIFFRACTION2(chain A and resid 25:89)
3X-RAY DIFFRACTION3(chain A and resid 90:125)
4X-RAY DIFFRACTION4(chain A and resid 126:150)
5X-RAY DIFFRACTION5(chain A and resid 151:171)

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