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- PDB-1kcu: CRYSTAL STRUCTURE OF ANTIBODY PC287 -

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Basic information

Entry
Database: PDB / ID: 1kcu
TitleCRYSTAL STRUCTURE OF ANTIBODY PC287
Components(PC287 IMMUNOGLOBULIN) x 2
KeywordsIMMUNE SYSTEM / ANTI-PEPTIDE ANTIBODY
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 / 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 ...Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / 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 / extracellular space / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
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/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 / :
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsNair, D.T. / Singh, K. / Siddiqui, Z. / Nayak, B.P. / Rao, K.V.S. / Salunke, D.M.
Citation
Journal: J.Immunol. / Year: 2002
Title: Epitope recognition by diverse antibodies suggests conformational convergence in an antibody response.
Authors: Nair, D.T. / Singh, K. / Siddiqui, Z. / Nayak, B.P. / Rao, K.V. / Salunke, D.M.
#1: Journal: 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: PC287 IMMUNOGLOBULIN
H: PC287 IMMUNOGLOBULIN


Theoretical massNumber of molelcules
Total (without water)46,6852
Polymers46,6852
Non-polymers00
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-22 kcal/mol
Surface area19340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.760, 71.635, 87.722
Angle α, β, γ (deg.)90.00, 98.14, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody PC287 IMMUNOGLOBULIN


Mass: 23478.830 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 PC287 IMMUNOGLOBULIN


Mass: 23205.986 Da / Num. of mol.: 1 / Fragment: heavy chain / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9R1A4, UniProt: P01869*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.46 Å3/Da / Density % sol: 49.91 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 15% PEG 8K, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
150 mMTris-Cl1reservoirpH7.2
20.05 %sodium azide1reservoir
310 mg/mlpeptide/Fab1drop

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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: 2.2→50 Å / Num. obs: 19589 / % possible obs: 85 % / Redundancy: 8 % / Biso Wilson estimate: 31.2 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.4
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 50 Å / Num. obs: 14215 / % possible obs: 85 % / Num. measured all: 157194 / Rmerge(I) obs: 0.1
Reflection shell
*PLUS
% possible obs: 81.8 % / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
MARdata collection
SCALEPACKdata scaling
AMoREphasing
CNS0.5refinement
MARdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→50 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 148770.82 / Data cutoff low absF: 0 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1203 6.9 %RANDOM
Rwork0.2 ---
obs-19589 85 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.8358 Å2 / ksol: 0.305654 e/Å3
Displacement parametersBiso mean: 33.6 Å2
Baniso -1Baniso -2Baniso -3
1-4.64 Å20 Å2-1.45 Å2
2---7.28 Å20 Å2
3---2.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3283 0 0 109 3392
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_d27.9
X-RAY DIFFRACTIONc_improper_angle_d1.56
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.363 156 6.5 %
Rwork0.311 2259 -
obs--63.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
Refinement
*PLUS
Rfactor obs: 0.2 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.593
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.56
LS refinement shell
*PLUS
Rfactor Rfree: 403 / Rfactor Rwork: 0.381 / Rfactor obs: 0.381

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