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- PDB-4po4: Crystal Structure of Lampetra planeri VLRC -

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Basic information

Entry
Database: PDB / ID: 4po4
TitleCrystal Structure of Lampetra planeri VLRC
ComponentsLampetra planeri VLRC
KeywordsIMMUNE SYSTEM / Jawless Vertebrate / VLRC / Leucine Rich Repeat / Variable Lymphocyte Receptor / Antigen Binding
Function / homology
Function and homology information


: / 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
Biological speciesLampetra planeri (European brook lamprey)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsGao, M.M. / Mariuzza, R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Selection of the lamprey VLRC antigen receptor repertoire.
Authors: Holland, S.J. / Gao, M. / Hirano, M. / Iyer, L.M. / Luo, M. / Schorpp, M. / Cooper, M.D. / Aravind, L. / Mariuzza, R.A. / Boehm, T.
History
DepositionFeb 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lampetra planeri VLRC
B: Lampetra planeri VLRC


Theoretical massNumber of molelcules
Total (without water)49,3082
Polymers49,3082
Non-polymers00
Water3,621201
1
A: Lampetra planeri VLRC


Theoretical massNumber of molelcules
Total (without water)24,6541
Polymers24,6541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lampetra planeri VLRC


Theoretical massNumber of molelcules
Total (without water)24,6541
Polymers24,6541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.319, 59.542, 66.324
Angle α, β, γ (deg.)90.000, 108.350, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lampetra planeri VLRC


Mass: 24654.121 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lampetra planeri (European brook lamprey)
Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: A0A088STQ5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.25 Å3/Da / Density % sol: 45.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1M SPG pH9, 20% PEG 1500, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 1, 2013
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→38.57 Å / Num. all: 15329 / Num. obs: 15329 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 21.95 Å2 / Rmerge(I) obs: 0.085 / Χ2: 0.97 / Net I/σ(I): 16.1 / Scaling rejects: 858
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.5-2.597.350.1769.41116315081.1699.2
2.59-2.697.380.1649.61145415411.0799.8
2.69-2.827.390.14810.91118315041.0499.7
2.82-2.967.380.13511.9114771540199.7
2.96-3.157.440.12612.61122915010.9999.7
3.15-3.397.460.10515.21144315180.9499.5
3.39-3.737.440.09217.71160815490.999.8
3.73-4.277.460.07821.21153515350.8799.9
4.27-5.387.440.06823.81157415440.8599.7
5.38-38.577.280.05627.91164015890.8499.8

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Processing

Software
NameVersionClassificationNB
d*TREK9.9.8.6 W9RSSIdata reduction
PHENIX1.8_1069refinement
PDB_EXTRACT3.14data extraction
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
PHASERMRphasing
RefinementResolution: 2.5→38.57 Å / FOM work R set: 0.8068 / SU ML: 0.29 / σ(F): 1.44 / Phase error: 25.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2492 765 5 %
Rwork0.2108 14548 -
obs0.2127 15313 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.09 Å2 / Biso mean: 14.34 Å2 / Biso min: 1.75 Å2
Refinement stepCycle: LAST / Resolution: 2.5→38.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3452 0 0 201 3653
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0213522
X-RAY DIFFRACTIONf_angle_d1.864778
X-RAY DIFFRACTIONf_chiral_restr0.143568
X-RAY DIFFRACTIONf_plane_restr0.008614
X-RAY DIFFRACTIONf_dihedral_angle_d15.161322
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.6930.33411370.256929123049100
2.693-2.96390.29721510.255128933044100
2.9639-3.39260.27771600.23928593019100
3.3926-4.27340.22311670.182329153082100
4.2734-38.57440.19651500.17932969311999

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