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- PDB-3rfj: Design of a binding scaffold based on variable lymphocyte recepto... -

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Basic information

Entry
Database: PDB / ID: 3rfj
TitleDesign of a binding scaffold based on variable lymphocyte receptors of jawless vertebrates by module engineering
ComponentsInternalin B, repeat modules, Variable lymphocyte receptor
KeywordsPROTEIN BINDING / LRR / plasma
Function / homology
Function and homology information


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, 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 ...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, 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
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
Petromyzon marinus (sea lamprey)
synthetic (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsKim, H.J. / Cheong, H.K. / Jeon, Y.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Design of a binding scaffold based on variable lymphocyte receptors of jawless vertebrates by module engineering
Authors: Lee, S.C. / Park, K. / Han, J. / Lee, J.J. / Kim, H.J. / Hong, S. / Heu, W. / Kim, Y.J. / Ha, J.S. / Lee, S.G. / Cheong, H.K. / Jeon, Y.H. / Kim, D. / Kim, H.S.
History
DepositionApr 6, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Internalin B, repeat modules, Variable lymphocyte receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4193
Polymers31,2271
Non-polymers1922
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.567, 60.836, 87.597
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 Internalin B, repeat modules, Variable lymphocyte receptor


Mass: 31227.279 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: chimera of Internalin B, repeat modules, Variable lymphocyte receptor
Source: (gene. exp.) Listeria monocytogenes (bacteria), (gene. exp.) Petromyzon marinus (sea lamprey), (gene. exp.) synthetic (others)
Strain: 08-5923 / Production host: Escherichia coli (E. coli) / References: UniProt: D2P9A6, UniProt: Q6E4K6
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE RESIDUE 66-213 REPRESENTS CONSENSUS DESIGNED REPEAT MODULES. THE SEQUENCES OF REPEAT MOLDUES IS ...THE RESIDUE 66-213 REPRESENTS CONSENSUS DESIGNED REPEAT MODULES. THE SEQUENCES OF REPEAT MOLDUES IS BASED ON VARIABLE LYMPHOCYTE RECEPTORS.

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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: 2.46 Å3/Da / Density % sol: 49.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 25.5% polyethylene glycol 4000, 15%(w/v) glycerol, 0.17M ammonium sulfate, pH 8.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 21, 2010
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→26.04 Å / Num. obs: 27691 / % possible obs: 91.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.8→1.86 Å / % possible all: 88.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→26.04 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.916 / SU B: 3.048 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26038 1482 5.1 %RANDOM
Rwork0.22166 ---
obs0.22366 27691 96.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Refinement stepCycle: LAST / Resolution: 1.78→26.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2105 0 10 97 2212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0222154
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2791.9832939
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.435267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.97726.35496
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.28115377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.513156
X-RAY DIFFRACTIONr_chiral_restr0.1750.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211596
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.291.51341
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.30922184
X-RAY DIFFRACTIONr_scbond_it3.9453813
X-RAY DIFFRACTIONr_scangle_it6.2544.5755
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.779→1.825 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 72 -
Rwork0.284 1705 -
obs--81.36 %

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