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- PDB-6bxd: Crystal structure of Variable Lymphocyte Receptor 2 (VLR2) -

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Basic information

Entry
Database: PDB / ID: 6bxd
TitleCrystal structure of Variable Lymphocyte Receptor 2 (VLR2)
ComponentsVariable Lymphocyte Receptor 2
KeywordsIMMUNE SYSTEM / VLR / LEUCINE-RICH REPEAT / lamprey antibody / immune receptor
Function / homologyChem-ETE
Function and homology information
Biological speciesPetromyzon marinus (sea lamprey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.103 Å
AuthorsGunn, R.J. / Wilson, I.A. / Cooper, M.D. / Herrin, B.R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)A1042266 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI072435 United States
CitationJournal: J. Mol. Biol. / Year: 2018
Title: VLR Recognition of TLR5 Expands the Molecular Characterization of Protein Antigen Binding by Non-Ig-based Antibodies.
Authors: Gunn, R.J. / Herrin, B.R. / Acharya, S. / Cooper, M.D. / Wilson, I.A.
History
DepositionDec 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Variable Lymphocyte Receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9933
Polymers22,6891
Non-polymers3042
Water4,792266
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.033, 74.731, 40.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Variable Lymphocyte Receptor 2 / / VLR2


Mass: 22688.521 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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ETE / 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL


Mass: 208.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20O5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O

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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: 2.15 Å3/Da / Density % sol: 42.67 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M (NH4)2SO4, 30% PEG 8K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.88557 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88557 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. obs: 74681 / % possible obs: 95.2 % / Redundancy: 9.5 % / Biso Wilson estimate: 12.8572207267 Å2 / CC1/2: 0.91 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.03 / Net I/av σ(I): 33.5 / Net I/σ(I): 33.4
Reflection shellResolution: 1.1→1.12 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2632 / Rpim(I) all: 0.37 / % possible all: 68.8

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TWI

3twi


Resolution: 1.103→37.365 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.179 3716 4.98 %
Rwork0.1768 --
obs0.1769 74609 95.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.103→37.365 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1446 0 19 266 1731
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041531
X-RAY DIFFRACTIONf_angle_d0.8192096
X-RAY DIFFRACTIONf_dihedral_angle_d16.275575
X-RAY DIFFRACTIONf_chiral_restr0.076252
X-RAY DIFFRACTIONf_plane_restr0.005267
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1027-1.11670.3008990.29411685X-RAY DIFFRACTION63
1.1167-1.13140.3111100.27981983X-RAY DIFFRACTION73
1.1314-1.14690.28641170.26132083X-RAY DIFFRACTION77
1.1469-1.16330.25811240.25492323X-RAY DIFFRACTION85
1.1633-1.18060.25341270.24572386X-RAY DIFFRACTION88
1.1806-1.19910.25421110.23412608X-RAY DIFFRACTION94
1.1991-1.21870.2131410.22652623X-RAY DIFFRACTION97
1.2187-1.23980.19431370.21972691X-RAY DIFFRACTION98
1.2398-1.26230.24951330.21892709X-RAY DIFFRACTION100
1.2623-1.28660.22181660.2042733X-RAY DIFFRACTION100
1.2866-1.31280.2041340.20592717X-RAY DIFFRACTION99
1.3128-1.34140.19751510.19382735X-RAY DIFFRACTION100
1.3414-1.37260.21381420.19262719X-RAY DIFFRACTION100
1.3726-1.40690.19621270.18852751X-RAY DIFFRACTION100
1.4069-1.4450.20221460.18772720X-RAY DIFFRACTION100
1.445-1.48750.17831320.18232741X-RAY DIFFRACTION100
1.4875-1.53550.18741580.17562767X-RAY DIFFRACTION100
1.5355-1.59040.19551430.16822736X-RAY DIFFRACTION100
1.5904-1.65410.17231140.1632794X-RAY DIFFRACTION100
1.6541-1.72930.15221500.1652728X-RAY DIFFRACTION99
1.7293-1.82050.19091590.17082724X-RAY DIFFRACTION99
1.8205-1.93460.17821570.16222777X-RAY DIFFRACTION100
1.9346-2.08390.17441560.15532765X-RAY DIFFRACTION100
2.0839-2.29360.16921300.15792786X-RAY DIFFRACTION99
2.2936-2.62540.15581540.16392782X-RAY DIFFRACTION99
2.6254-3.30740.15211460.1742847X-RAY DIFFRACTION100
3.3074-37.3870.17181520.17372980X-RAY DIFFRACTION99
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)
18.71171.96930.14537.78572.10986.60860.20530.0266-0.06610.0913-0.10260.52680.2465-0.685-0.12460.1562-0.00480.00140.16250.03910.202-72.9083-1.139568.0168
21.2702-0.54020.21521.43450.16190.595-0.0197-0.1228-0.0325-0.02480.01090.1302-0.0487-0.17380.01250.09680.00950.0070.12060.00580.1207-73.44947.878763.3578
31.19090.06740.40810.4468-0.21691.6345-0.0293-0.00470.0743-0.02010.03430.0155-0.1222-0.0513-0.00630.10390.00210.00180.1006-0.00130.1173-64.660713.993757.7873
42.0099-0.40920.86832.12930.41083.0894-0.00610.04340.0763-0.0475-0.02170.0365-0.1768-0.07360.03380.065-0.02020.02190.08430.00950.1042-57.436719.762950.713
51.8067-0.24590.50142.342-0.35692.3722-0.00530.2182-0.0544-0.1485-0.0021-0.01820.08110.09110.00730.0822-0.00820.01060.125-0.00530.0963-51.736619.02146.1326
62.7484-0.7346-0.33567.5532-0.22055.98130.03230.25640.2938-0.56570.06090.3433-0.5534-0.3153-0.06110.191-0.0045-0.01030.14490.02820.1781-56.562529.416339.3237
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 36 )
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 77 )
3X-RAY DIFFRACTION3chain 'A' and (resid 78 through 134 )
4X-RAY DIFFRACTION4chain 'A' and (resid 135 through 163 )
5X-RAY DIFFRACTION5chain 'A' and (resid 164 through 199 )
6X-RAY DIFFRACTION6chain 'A' and (resid 200 through 212 )

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