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- PDB-3m19: Crystal structure of variable lymphocyte receptor VLRA.R5.1 -

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Basic information

Entry
Database: PDB / ID: 3m19
TitleCrystal structure of variable lymphocyte receptor VLRA.R5.1
ComponentsVariable lymphocyte receptor A diversity region
KeywordsIMMUNE SYSTEM / variable lymphocyte receptor / adaptive immunity / antibody / T cell / B cell / leucine-rich repeat
Function / homology
Function and homology information


Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / 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 / Alpha Beta
Similarity search - Domain/homology
Variable lymphocyte receptor A diversity region
Similarity search - Component
Biological speciesPetromyzon marinus (sea lamprey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsDeng, L. / Velikovsky, C.A. / Mariuzza, R.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: A structural basis for antigen recognition by the T cell-like lymphocytes of sea lamprey.
Authors: Deng, L. / Velikovsky, C.A. / Xu, G. / Iyer, L.M. / Tasumi, S. / Kerzic, M.C. / Flajnik, M.F. / Aravind, L. / Pancer, Z. / Mariuzza, R.A.
History
DepositionMar 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Variable lymphocyte receptor A diversity region
B: Variable lymphocyte receptor A diversity region


Theoretical massNumber of molelcules
Total (without water)54,9562
Polymers54,9562
Non-polymers00
Water5,909328
1
A: Variable lymphocyte receptor A diversity region


Theoretical massNumber of molelcules
Total (without water)27,4781
Polymers27,4781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Variable lymphocyte receptor A diversity region


Theoretical massNumber of molelcules
Total (without water)27,4781
Polymers27,4781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.333, 77.053, 65.392
Angle α, β, γ (deg.)90.00, 112.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Variable lymphocyte receptor A diversity region


Mass: 27477.963 Da / Num. of mol.: 2 / Fragment: Ectodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Petromyzon marinus (sea lamprey) / Gene: VLRA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus(DE3) / References: UniProt: C7B6Z3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 42.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 20% (w/v) polyethylene glycol 6000, 1.0 M LiCl and 0.1 M citric acid, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 48278 / Redundancy: 3.7 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 12.9
Reflection shellResolution: 1.7→1.82 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3M18
Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.928 / SU B: 2.523 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25494 2561 5 %RANDOM
Rwork0.20944 ---
obs0.21175 48278 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.207 Å2
Baniso -1Baniso -2Baniso -3
1--1.31 Å20 Å2-0.65 Å2
2--2.23 Å20 Å2
3----1.41 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3632 0 0 328 3960
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223705
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6261.9835026
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1165474
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.58326.196163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20515670
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7211515
X-RAY DIFFRACTIONr_chiral_restr0.1080.2600
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022723
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2220.21680
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.22503
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2285
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.269
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1351.52408
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.78723785
X-RAY DIFFRACTIONr_scbond_it3.04531431
X-RAY DIFFRACTIONr_scangle_it4.7754.51239
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 189 -
Rwork0.255 3597 -
obs--100 %

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