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- PDB-3g3b: Structure of a lamprey variable lymphocyte receptor mutant in com... -

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Basic information

Entry
Database: PDB / ID: 3g3b
TitleStructure of a lamprey variable lymphocyte receptor mutant in complex with a protein antigen
Components
  • Lysozyme C
  • variable lymphocyte receptor VLRB.2D
KeywordsHYDROLASE/IMMUNE SYSTEM / VLR / antibody / Allergen / Antimicrobial / Bacteriolytic enzyme / Glycosidase / Hydrolase / HYDROLASE-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
Variable lymphocyte receptor, C-terminal / Domain of unknown function (DUF3439) / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype ...Variable lymphocyte receptor, C-terminal / Domain of unknown function (DUF3439) / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / 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 / Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Leucine-rich repeat domain superfamily / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Variable lymphocyte receptor VLRB.2D / Lysozyme C
Similarity search - Component
Biological speciesPetromyzon marinus (sea lamprey)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDeng, L. / Velikovsky, C.A. / Mariuzza, R.A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Structure of a lamprey variable lymphocyte receptor in complex with a protein antigen.
Authors: Velikovsky, C.A. / Deng, L. / Tasumi, S. / Iyer, L.M. / Kerzic, M.C. / Aravind, L. / Pancer, Z. / Mariuzza, R.A.
History
DepositionFeb 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: 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
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 VLRB.2D
B: Lysozyme C
C: variable lymphocyte receptor VLRB.2D
D: Lysozyme C
E: variable lymphocyte receptor VLRB.2D
F: Lysozyme C
G: variable lymphocyte receptor VLRB.2D
H: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)132,2068
Polymers132,2068
Non-polymers00
Water3,243180
1
A: variable lymphocyte receptor VLRB.2D
B: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)33,0512
Polymers33,0512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: variable lymphocyte receptor VLRB.2D
D: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)33,0512
Polymers33,0512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: variable lymphocyte receptor VLRB.2D
F: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)33,0512
Polymers33,0512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: variable lymphocyte receptor VLRB.2D
H: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)33,0512
Polymers33,0512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.874, 106.244, 218.544
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
variable lymphocyte receptor VLRB.2D


Mass: 18720.240 Da / Num. of mol.: 4 / Fragment: variable lymphocyte receptor 2D13 / Mutation: Q40R, K101R, G132W, P142H, E159K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Petromyzon marinus (sea lamprey) / Gene: vlr / Plasmid: pT7.7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: D0VX19*PLUS
#2: Protein
Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV


Mass: 14331.160 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Strain: Chicken / Gene: lysozyme, LYZ / Production host: Escherichia coli (E. coli) / References: UniProt: P00698, lysozyme
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.76 Å3/Da / Density % sol: 55.44 %
Crystal growTemperature: 296 K / Method: evaporation / pH: 8.5
Details: 8% (w/v) polyethylene glycol 8000, 0.1 M Tris-HCl, pH 8.5, EVAPORATION, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 60645 / Redundancy: 13.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 29.1
Reflection shellResolution: 2.4→2.48 Å / Redundancy: 14 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 6.7

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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 3G3A

3g3a


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.886 / SU B: 8.899 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.373 / ESU R Free: 0.274 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28612 2921 5 %RANDOM
Rwork0.24202 ---
obs0.24426 55191 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.722 Å2
Baniso -1Baniso -2Baniso -3
1--1.92 Å20 Å20 Å2
2--0.11 Å20 Å2
3---1.81 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8291 0 0 180 8471
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0218479
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6151.93211536
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.58251045
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.30523.517381
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.741151366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3651569
X-RAY DIFFRACTIONr_chiral_restr0.110.21296
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026393
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2210.23708
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.25576
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2328
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8351.55423
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.44328481
X-RAY DIFFRACTIONr_scbond_it2.18433598
X-RAY DIFFRACTIONr_scangle_it3.2874.53055
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 205 -
Rwork0.297 4021 -
obs--99.98 %

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