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- PDB-1kcv: Crystal structure of antibody pc282 -

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Basic information

Entry
Database: PDB / ID: 1kcv
TitleCrystal structure of antibody pc282
Components(PC282 IMMUNOGLOBULIN) x 2
KeywordsIMMUNE SYSTEM / ANTI-PEPTIDE ANTIBODY / FAB FRAGMENT
Function / homology
Function and homology information


immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / B cell differentiation / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / : / 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 heavy chain V region 1B43
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNair, D.T. / Singh, K. / Siddiqui, Z. / Nayak, B.P. / Rao, K.V. / 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
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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: PC282 IMMUNOGLOBULIN
H: PC282 IMMUNOGLOBULIN


Theoretical massNumber of molelcules
Total (without water)45,7442
Polymers45,7442
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-20 kcal/mol
Surface area18860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.646, 72.939, 58.550
Angle α, β, γ (deg.)90.00, 100.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody PC282 IMMUNOGLOBULIN


Mass: 22983.266 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 PC282 IMMUNOGLOBULIN


Mass: 22760.301 Da / Num. of mol.: 1 / Fragment: heavy chain / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P18532
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.42 Å3/Da / Density % sol: 49.07 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 10 % PEG 3K, 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: 1.8→50 Å / Num. obs: 36471 / % possible obs: 91 % / Redundancy: 10.3 % / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 10.5
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 50 Å / % possible obs: 91 % / Num. measured all: 378203
Reflection shell
*PLUS
% possible obs: 83.2 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 3.4

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Processing

Software
NameVersionClassification
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
CNS0.5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→50 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 273586.43 / Data cutoff low absF: 0 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.233 3647 10 %RANDOM
Rwork0.203 ---
obs-36471 91 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.6569 Å2 / ksol: 0.304702 e/Å3
Displacement parametersBiso mean: 26.7 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3210 0 0 69 3279
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d27.8
X-RAY DIFFRACTIONc_improper_angle_d1.27
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.334 541 10.7 %
Rwork0.298 4495 -
obs--76 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 50 Å / Rfactor obs: 0.203
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.379
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.27
LS refinement shell
*PLUS
Rfactor obs: 0.298

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