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- PDB-1kcr: CRYSTAL STRUCTURE OF ANTIBODY PC283 IN COMPLEX WITH PS1 PEPTIDE -

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Basic information

Entry
Database: PDB / ID: 1kcr
TitleCRYSTAL STRUCTURE OF ANTIBODY PC283 IN COMPLEX WITH PS1 PEPTIDE
Components
  • (PC283 IMMUNOGLOBULIN) x 2
  • PS1 peptide
KeywordsIMMUNE SYSTEM / ANTIBODY / PEPTIDE ANTIGEN COMPLEX (ANTIBODY-PEPTIDE)
Function / homology
Function and homology information


Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / caveolin-mediated endocytosis of virus by host cell / Regulation of actin dynamics for phagocytic cup formation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity ...Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / caveolin-mediated endocytosis of virus by host cell / Regulation of actin dynamics for phagocytic cup formation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / phagocytosis, engulfment / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / immunoglobulin mediated immune response / positive regulation of phagocytosis / complement activation, classical pathway / antigen binding / B cell differentiation / positive regulation of immune response / antibacterial humoral response / defense response to bacterium / external side of plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / extracellular space / extracellular region / membrane / plasma membrane / cytoplasm
Similarity search - Function
Large envelope protein S / Major surface antigen from hepadnavirus / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily ...Large envelope protein S / Major surface antigen from hepadnavirus / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Immunoglobulin kappa constant / Ig gamma-1 chain C region, membrane-bound form / Large envelope protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsNair, D.T. / Singh, K. / Sahu, N. / Rao, K.V.S. / Salunke, D.M.
CitationJournal: J.Immunol. / Year: 2000
Title: Crystal structure of an antibody bound to an immunodominant peptide epitope: novel features in peptide-antibody recognition.
Authors: Nair, D.T. / Singh, K. / Sahu, N. / Rao, K.V. / Salunke, D.M.
History
DepositionNov 11, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 999SEQUENCE An appropriate sequence database match for the Immunoglobulin was not available at the ...SEQUENCE An appropriate sequence database match for the Immunoglobulin was not available at the time of processing.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: PC283 IMMUNOGLOBULIN
H: PC283 IMMUNOGLOBULIN
P: PS1 peptide


Theoretical massNumber of molelcules
Total (without water)47,8463
Polymers47,8463
Non-polymers00
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-32 kcal/mol
Surface area19580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.724, 72.686, 84.493
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: Antibody PC283 IMMUNOGLOBULIN


Mass: 23279.693 Da / Num. of mol.: 1 / Fragment: light chain / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01837
#2: Antibody PC283 IMMUNOGLOBULIN


Mass: 22981.807 Da / Num. of mol.: 1 / Fragment: heavy chain / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01869
#3: Protein/peptide PS1 peptide


Mass: 1584.622 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Hepatitis B virus.
References: GenBank: 15419846, UniProt: Q91C35*PLUS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.24 Å3/Da / Density % sol: 44.99 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 18% PEG 3K, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1dropwith a 20-fold molar excess of peptide
250 mMTris-Cl1droppH7.2
318 %PEG33001reservoir

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 9651 / Num. obs: 7953 / % possible obs: 82 % / Redundancy: 1.4 % / Biso Wilson estimate: 37.5 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 5.1
Reflection
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 50 Å / % possible obs: 82 % / Num. measured all: 11134
Reflection shell
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 3.03 Å / % possible obs: 61.1 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
MARdata collection
SCALEPACKdata scaling
AMoREphasing
CNS0.5refinement
MARdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→50 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 146232.66 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.277 785 10.6 %RANDOM
Rwork0.184 ---
all-7953 --
obs-7953 82.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 19.185 Å2 / ksol: 0.219768 e/Å3
Displacement parametersBiso mean: 24.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20 Å2
2---0.81 Å20 Å2
3---0.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3363 0 0 31 3394
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.306
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d27.2
X-RAY DIFFRACTIONc_improper_angle_d1.21
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.326 93 11.3 %
Rwork0.305 731 -
obs--51 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 100 Å / Rfactor obs: 0.188 / Rfactor Rfree: 0.261 / Rfactor Rwork: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.571
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.21
LS refinement shell
*PLUS
Lowest resolution: 3.03 Å / Rfactor Rfree: 0.375 / Rfactor Rwork: 0.272 / Rfactor obs: 0.272

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