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- PDB-6bxe: Crystal structure of Variable Lymphocyte Receptor 9 (VLR9) -

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Basic information

Entry
Database: PDB / ID: 6bxe
TitleCrystal structure of Variable Lymphocyte Receptor 9 (VLR9)
ComponentsVariable lymphocyte receptor diversity region
KeywordsIMMUNE SYSTEM / VLR / LEUCINE-RICH REPEAT / lamprey antibody / immune receptor
Function / homologyLeucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Variable lymphocyte receptor diversity region
Function and homology information
Biological speciesPetromyzon marinus (sea lamprey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.651 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)AI042266 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 1.4Mar 30, 2022Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.grant_number
Revision 1.5Oct 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 diversity region
B: Variable lymphocyte receptor diversity region


Theoretical massNumber of molelcules
Total (without water)38,5752
Polymers38,5752
Non-polymers00
Water5,296294
1
A: Variable lymphocyte receptor diversity region


Theoretical massNumber of molelcules
Total (without water)19,2881
Polymers19,2881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Variable lymphocyte receptor diversity region


Theoretical massNumber of molelcules
Total (without water)19,2881
Polymers19,2881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.511, 75.511, 99.307
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

#1: Protein Variable lymphocyte receptor diversity region


Mass: 19287.643 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Petromyzon marinus (sea lamprey) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A5HBR7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 42.77 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 2.0 M (NH4)2SO4, 0.1 M citrate pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 38111 / % possible obs: 98.9 % / Redundancy: 18.3 % / CC1/2: 0.95 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.02 / Net I/σ(I): 38.2
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1669 / CC1/2: 0.68 / Rpim(I) all: 0.28 / % possible all: 86.6

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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: 1.651→35.291 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 17.18
RfactorNum. reflection% reflection
Rfree0.1735 1854 4.87 %
Rwork0.1528 --
obs0.1538 38071 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.651→35.291 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 0 294 2726
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072493
X-RAY DIFFRACTIONf_angle_d0.9153418
X-RAY DIFFRACTIONf_dihedral_angle_d11.7851501
X-RAY DIFFRACTIONf_chiral_restr0.061403
X-RAY DIFFRACTIONf_plane_restr0.006439
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6515-1.69610.2331120.22862512X-RAY DIFFRACTION89
1.6961-1.7460.26651200.20452766X-RAY DIFFRACTION98
1.746-1.80240.25981320.1922824X-RAY DIFFRACTION100
1.8024-1.86680.20641710.17582765X-RAY DIFFRACTION100
1.8668-1.94150.18061540.16232799X-RAY DIFFRACTION100
1.9415-2.02990.17261820.14662767X-RAY DIFFRACTION100
2.0299-2.13690.15561460.14692801X-RAY DIFFRACTION100
2.1369-2.27080.18191060.14692856X-RAY DIFFRACTION100
2.2708-2.44610.17921280.1452840X-RAY DIFFRACTION100
2.4461-2.69210.16761790.15492779X-RAY DIFFRACTION100
2.6921-3.08150.18981410.16212803X-RAY DIFFRACTION100
3.0815-3.88160.15151500.14272832X-RAY DIFFRACTION100
3.8816-35.2990.15931330.14142873X-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)
14.6342-1.27640.30726.558-0.01294.9041-0.1885-0.98890.41510.60860.25260.1969-0.5321-0.3621-0.13150.30560.0417-0.0030.4735-0.08850.2198-3.775-28.27789.012
22.50830.8470.43652.9651-0.66571.95360.0009-0.44030.45140.34280.01070.1406-0.2619-0.2104-0.02220.21940.02870.0040.2891-0.08750.2291-1.7467-22.35532.1668
31.88380.06620.18532.2815-2.00442.5258-0.0801-0.37780.37620.64550.1314-0.2621-0.25160.103-0.13540.18530.0082-0.03850.2013-0.07770.22649.3422-25.27262.8319
42.4287-0.00080.22090.6112-0.42121.84780.03960.00010.183-0.012-0.0012-0.032-0.0723-0.0012-0.07450.1560.0027-0.01360.1529-0.0240.20014.3147-23.8983-10.2992
55.82350.580.23755.3863-3.04285.68920.01740.36150.1633-0.4048-0.224-0.55010.35110.45660.13960.21160.04570.03250.29170.00060.21339.8328-25.6012-20.0757
63.3674-1.38932.0630.7041-0.56852.43750.00460.34830.1964-0.2126-0.10940.17360.0890.08460.21140.28510.0252-0.01450.2521-0.00040.2313-1.2756-23.2787-23.9527
75.4733.08210.6088.1438-0.50595.32260.02430.57480.9981-0.7501-0.4435-0.7707-0.44170.5680.51380.28040.06820.02630.38320.14470.53278.8562-15.2918-26.5287
81.69521.92242.41782.35982.86393.58530.33610.04130.0421-0.0833-0.2937-0.49240.26630.68-0.05440.38850.0478-0.01780.35150.10390.39586.1403-49.86062.7558
92.27960.27731.24592.74470.57873.23260.14030.08130.0021-0.0983-0.1927-0.45860.23460.35610.03470.24140.05040.01020.27320.07750.2641.6513-47.2662-2.0364
102.81450.3333-0.30412.8942-0.2173.1573-0.07080.0752-0.1652-0.1194-0.0851-0.05880.46240.02520.12690.27540.01910.01440.20850.0360.2159-7.2964-48.456-7.4059
112.62670.8697-0.33632.9332-0.73582.7842-0.0262-0.1150.0749-0.0622-0.03520.24360.15510.02770.07140.17880.0077-0.00440.1920.03290.2084-13.4726-41.7513-7.7925
122.9551-2.5357-0.51852.8781-0.14675.12470.0590.22-0.1857-0.4431-0.06970.45790.2531-0.05170.01620.297-0.0136-0.03420.22120.01590.2717-15.8832-42.8882-21.3232
135.47052.53092.12315.93660.71225.0337-0.0487-0.1178-0.1248-0.14180.06530.50020.1973-0.7403-0.05290.1895-0.015-0.01840.30350.04930.2507-22.6299-38.8695-12.7385
145.24470.8577-0.4638.07881.30780.75350.03620.3501-0.0223-0.6698-0.1120.07070.0282-0.20430.00120.25070.0183-0.01780.21670.04290.1937-16.0142-35.0905-22.1003
154.9131.97390.86165.64621.13683.1413-0.01740.5254-0.6789-0.43290.15611.04960.798-0.7314-0.10030.4696-0.1553-0.14920.4148-0.02920.531-26.7513-43.1873-22.931
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 34 )
2X-RAY DIFFRACTION2chain 'A' and (resid 35 through 65 )
3X-RAY DIFFRACTION3chain 'A' and (resid 66 through 75 )
4X-RAY DIFFRACTION4chain 'A' and (resid 76 through 137 )
5X-RAY DIFFRACTION5chain 'A' and (resid 138 through 153 )
6X-RAY DIFFRACTION6chain 'A' and (resid 154 through 166 )
7X-RAY DIFFRACTION7chain 'A' and (resid 167 through 181 )
8X-RAY DIFFRACTION8chain 'B' and (resid 17 through 26 )
9X-RAY DIFFRACTION9chain 'B' and (resid 27 through 55 )
10X-RAY DIFFRACTION10chain 'B' and (resid 56 through 94 )
11X-RAY DIFFRACTION11chain 'B' and (resid 95 through 127 )
12X-RAY DIFFRACTION12chain 'B' and (resid 128 through 137 )
13X-RAY DIFFRACTION13chain 'B' and (resid 138 through 153 )
14X-RAY DIFFRACTION14chain 'B' and (resid 154 through 166 )
15X-RAY DIFFRACTION15chain 'B' and (resid 167 through 181 )

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