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- PDB-3g3a: Structure of a lamprey variable lymphocyte receptor in complex wi... -

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Basic information

Entry
Database: PDB / ID: 3g3a
TitleStructure of a lamprey variable lymphocyte receptor 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


Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / 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. / Lysozyme - #10 / Leucine-rich repeat / 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: 2.2 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
Revision 1.3Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)134,7808
Polymers134,7808
Non-polymers00
Water10,413578
1
A: Variable lymphocyte receptor VLRB.2D
B: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)33,6952
Polymers33,6952
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)33,6952
Polymers33,6952
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)33,6952
Polymers33,6952
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)33,6952
Polymers33,6952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.299, 133.651, 90.439
Angle α, β, γ (deg.)90.00, 114.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Variable lymphocyte receptor VLRB.2D


Mass: 19363.932 Da / Num. of mol.: 4 / Fragment: Ectodomain
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: D0VX18*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


Mass: 18.015 Da / Num. of mol.: 578 / 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: 3.35 Å3/Da / Density % sol: 63.32 %
Crystal growTemperature: 296 K / Method: evaporation / pH: 5.6
Details: 2.0 M ammonium sulfate and 0.1 M sodium citrate, pH 5.6, 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: 2.2→50 Å / Num. obs: 88576 / Redundancy: 4.3 % / Biso Wilson estimate: 23.7 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 12.6
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 3.2 / Num. unique all: 5760

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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 3G39

3g39


Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.879 / SU B: 5.931 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.225 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27068 4460 5 %RANDOM
Rwork0.21954 ---
obs0.22211 84142 98.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.014 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20.45 Å2
2---1.19 Å20 Å2
3---1.65 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8959 0 0 578 9537
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0229166
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7551.94112490
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.69651155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.04524.171398
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.083151475
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.2441564
X-RAY DIFFRACTIONr_chiral_restr0.1180.21412
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026920
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2210.24344
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.26140
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.2656
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.238
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2340.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9391.55933
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.57129333
X-RAY DIFFRACTIONr_scbond_it2.54733749
X-RAY DIFFRACTIONr_scangle_it3.8144.53157
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 323 -
Rwork0.246 6070 -
obs--96.24 %

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