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- PDB-2y06: CRYSTAL STRUCTURE ANALYSIS OF THE ANTI-(4-HYDROXY-3-NITROPHENYL) ... -

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Basic information

Entry
Database: PDB / ID: 2y06
TitleCRYSTAL STRUCTURE ANALYSIS OF THE ANTI-(4-HYDROXY-3-NITROPHENYL) - ACETYL MURINE GERMLINE ANTIBODY BBE6.12H3 FAB FRAGMENT IN COMPLEX WITH A PHAGE DISPLAY DERIVED DODECAPEPTIDE GDPRPSYISHLL
Components
  • ANTI-NP MURINE GERMLINE MONOCLONAL ANTIBODY BBE6.12H3, HEAVY CHAIN
  • ANTI-NP MURINE GERMLINE MONOCLONAL ANTIBODY BBE6.12H3, LIGHT CHAIN
  • PHAGE DISPLAY DERIVED ANTIGEN
KeywordsIMMUNE SYSTEM / BETA-SANDWICH IMMUNOGLOBULIN FOLD / ANTIGEN BINDING / SECRETED PROTEIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMUS MUSCULUS (house mouse)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKhan, T. / Salunke, D.M.
CitationJournal: J.Immunol. / Year: 2012
Title: Structural Elucidation of the Mechanistic Basis of Degeneracy in the Primary Humoral Response.
Authors: Khan, T. / Salunke, D.M.
History
DepositionNov 30, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2012Group: Other
Revision 1.2Oct 16, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status / reflns_shell
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.status_code_sf / _reflns_shell.Rmerge_I_obs
Revision 1.3May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: ANTI-NP MURINE GERMLINE MONOCLONAL ANTIBODY BBE6.12H3, HEAVY CHAIN
L: ANTI-NP MURINE GERMLINE MONOCLONAL ANTIBODY BBE6.12H3, LIGHT CHAIN
P: PHAGE DISPLAY DERIVED ANTIGEN


Theoretical massNumber of molelcules
Total (without water)47,3543
Polymers47,3543
Non-polymers00
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-31.3 kcal/mol
Surface area19130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.570, 61.880, 112.500
Angle α, β, γ (deg.)90.00, 90.55, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody ANTI-NP MURINE GERMLINE MONOCLONAL ANTIBODY BBE6.12H3, HEAVY CHAIN


Mass: 23458.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell: B-CELLS / Cell line: BBE6.12H3 MURINE HYBRIDOMA / Organ: SPLEEN / Strain: C57BL/6
#2: Antibody ANTI-NP MURINE GERMLINE MONOCLONAL ANTIBODY BBE6.12H3, LIGHT CHAIN


Mass: 22538.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell: B-CELLS / Cell line: BBE6.12H3 MURINE HYBRIDOMA / Organ: SPLEEN / Strain: C57BL/6
#3: Protein/peptide PHAGE DISPLAY DERIVED ANTIGEN


Mass: 1356.528 Da / Num. of mol.: 1 / Fragment: PEPTIDE, RESIDUES 1-12 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 1.93 Å3/Da / Density % sol: 36.46 % / Description: NONE
Crystal growTemperature: 301 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 0.05 M TRIS HCL, 0.025% SODIUM AZIDE, PEG 8000., pH 7.1

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 12, 2009 / Details: BENT COLLIMATING MIRROR AND TOROID
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.5→41.3 Å / Num. obs: 13312 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 59 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10
Reflection shellResolution: 2.5→7.9 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2.5 / % possible all: 99.3

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Processing

Software
NameVersionClassification
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NATIVE FAB STRUCTURE

Resolution: 2.5→41.3 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 137292.07 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2663 1213 9.1 %RANDOM
Rwork0.2339 ---
obs0.2339 11673 87.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.968 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 68 Å2
Baniso -1Baniso -2Baniso -3
1-1.173 Å20 Å2-9.683 Å2
2--10.76 Å20 Å2
3----11.933 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.5→41.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3269 0 0 45 3314
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008581
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.71209
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d28.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.9
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 24
RfactorNum. reflection% reflection
Rfree0.36 245 11.1 %
Rwork0.34 1460 -
obs--78.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR PROTEIN_REP.PARAMCNS_TOPPAR PROTEIN.TOP
X-RAY DIFFRACTION2CNS_TOPPAR WATER_REP.PARAMCNS_TOPPAR WATER.TOP
X-RAY DIFFRACTION3TRIS.PARAM
X-RAY DIFFRACTION4CNS_TOPPAR ION.PARAM

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