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- PDB-3wo9: Crystal structure of the lamprey variable lymphocyte receptor C -

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Basic information

Entry
Database: PDB / ID: 3wo9
TitleCrystal structure of the lamprey variable lymphocyte receptor C
ComponentsVariable lymphocyte receptor C
KeywordsIMMUNE SYSTEM / Leucine rich repeat / immunological receptor / Membrane
Function / homology
Function and homology information


: / Leucine 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 profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
Variable lymphocyte receptor C
Similarity search - Component
Biological speciesLethenteron camtschaticum (Arctic lamprey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKanda, R. / Sutoh, Y. / Kasamatsu, J. / Maenaka, K. / Kasahara, M. / Ose, T.
CitationJournal: Plos One / Year: 2014
Title: Crystal structure of the lamprey variable lymphocyte receptor C reveals an unusual feature in its N-terminal capping module.
Authors: Kanda, R. / Sutoh, Y. / Kasamatsu, J. / Maenaka, K. / Kasahara, M. / Ose, T.
History
DepositionDec 20, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.2Nov 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: Variable lymphocyte receptor C


Theoretical massNumber of molelcules
Total (without water)27,5451
Polymers27,5451
Non-polymers00
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.157, 37.229, 55.133
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Variable lymphocyte receptor C


Mass: 27544.906 Da / Num. of mol.: 1 / Fragment: VLRC ectodomain, UNP RESIDUES 25-246
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lethenteron camtschaticum (Arctic lamprey)
Gene: VLRC / Plasmid: pET-26(b) / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: E0D2V6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 1.9 Å3/Da / Density % sol: 35.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% PEG 3350, 0.2M potassium phosphate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 29, 2011 / Details: mirrors
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 9798 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 16.63 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 11.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 4.1 / Num. unique all: 885 / % possible all: 92.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O6Q

2o6q


Resolution: 2.3→37.469 Å / SU ML: 0.25 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / σ(I): 0 / Phase error: 22.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2381 476 4.87 %RANDOM
Rwork0.1814 ---
obs0.1842 9769 99.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.6 Å2
Refinement stepCycle: LAST / Resolution: 2.3→37.469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1710 0 0 101 1811
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031740
X-RAY DIFFRACTIONf_angle_d0.7622365
X-RAY DIFFRACTIONf_dihedral_angle_d13.902638
X-RAY DIFFRACTIONf_chiral_restr0.054289
X-RAY DIFFRACTIONf_plane_restr0.002308
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3001-2.63280.27321500.1805296497
2.6328-3.31670.24671520.19513102100
3.3167-37.47440.22091740.17393227100

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