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- PDB-1dl7: THE STRUCTURAL BASIS OF REPERTOIRE SHIFT IN AN IMMUNE RESPONSE TO... -

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Basic information

Entry
Database: PDB / ID: 1dl7
TitleTHE STRUCTURAL BASIS OF REPERTOIRE SHIFT IN AN IMMUNE RESPONSE TO PHOSPHOCHOLINE
Components
  • PROTEIN (ANTIBODY M3C65 (HEAVY CHAIN))
  • PROTEIN (ANTIBODY M3C65 (LIGHT CHAIN))
KeywordsIMMUNE SYSTEM / SINGLE CHAIN FV / REPERTOIRE SHIFT
Function / homology
Function and homology information


immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / adaptive immune response / blood microparticle / immune response / extracellular space
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
P-NITROPHENYL-PHOSPHOCHOLINE / Ig lambda-1 chain V regions MOPC 104E/RPC20/J558/S104 / Ig heavy chain V region PJ14
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.35 Å
AuthorsSchumacher, M. / Brown, M.
CitationJournal: J.Exp.Med. / Year: 2000
Title: The structural basis of repertoire shift in an immune response to phosphocholine.
Authors: Brown, M. / Schumacher, M.A. / Wiens, G.D. / Brennan, R.G. / Rittenberg, M.B.
History
DepositionDec 8, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 2, 2013Group: Source and taxonomy
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: PROTEIN (ANTIBODY M3C65 (LIGHT CHAIN))
H: PROTEIN (ANTIBODY M3C65 (HEAVY CHAIN))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1843
Polymers23,8792
Non-polymers3051
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-10 kcal/mol
Surface area10840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.900, 35.900, 50.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO H 101
Detailsthe biological assembly is a dimer of one light chain and one heavy chain.

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Components

#1: Antibody PROTEIN (ANTIBODY M3C65 (LIGHT CHAIN))


Mass: 11544.834 Da / Num. of mol.: 1 / Fragment: FV (SINGLE CHAIN)
Source method: isolated from a genetically manipulated source
Details: COMBINED LIGHT AND HEAVY CHAIN VIA (G4S)3 LINKER / Source: (gene. exp.) Mus musculus (house mouse) / Gene: HYBRIDOMA M3C65 / Plasmid: PET3D / Production host: Escherichia coli (E. coli) / References: UniProt: P01724*PLUS
#2: Antibody PROTEIN (ANTIBODY M3C65 (HEAVY CHAIN))


Mass: 12333.841 Da / Num. of mol.: 1 / Fragment: FV (SINGLE CHAIN)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: HYBRIDOMA M3C65 / Plasmid: PET3D / Production host: Escherichia coli (E. coli) / References: UniProt: P01820*PLUS
#3: Chemical ChemComp-NCH / P-NITROPHENYL-PHOSPHOCHOLINE


Mass: 305.244 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N2O6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.48 Å3/Da / Density % sol: 50.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: SODIUM/POTASSIUM PHOSPHATE, HEPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15.6 mg/mlprotein1drop
22 mMNPPC1drop
31.5 M1reservoirNaH2PO4/K2HPO4
40.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→10 Å / Num. all: 47930 / Num. obs: 8983 / % possible obs: 84 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 8.5
Reflection shellResolution: 2.35→2.42 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3 / % possible all: 52
Reflection
*PLUS
Num. measured all: 47930
Reflection shell
*PLUS
% possible obs: 47 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 1.5

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Processing

Software
NameClassification
bioteXdata collection
bioteXdata reduction
EPMRphasing
TNTrefinement
bioteXdata scaling
RefinementResolution: 2.35→10 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.265 43 -RANDOM
Rwork0.189 ---
all0.189 47930 --
obs0.191 8983 84 %-
Refinement stepCycle: LAST / Resolution: 2.35→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1680 0 20 79 1779
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.014
X-RAY DIFFRACTIONt_angle_deg1.9
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS

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