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- PDB-2y36: Crystal structure analysis of the anti-(4-hydroxy-3-nitrophenyl)-... -

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Basic information

Entry
Database: PDB / ID: 2y36
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 DLWTTAIPTIPS
Components
  • (ANTI-NP MURINE GERMLINE MONOCLONAL ANTIBODY BBE6.12H3) x 2
  • DODECAPEPTIDE (DLWTTAIPTIPS)
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: 2.7 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
DepositionDec 18, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2012Group: Other
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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
L: ANTI-NP MURINE GERMLINE MONOCLONAL ANTIBODY BBE6.12H3
P: DODECAPEPTIDE (DLWTTAIPTIPS)


Theoretical massNumber of molelcules
Total (without water)47,4943
Polymers47,4943
Non-polymers00
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-31.5 kcal/mol
Surface area19150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.010, 63.620, 113.380
Angle α, β, γ (deg.)90.00, 90.40, 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


Mass: 23640.480 Da / Num. of mol.: 1 / Fragment: ANTIGEN-BINDING FRAGMENT, RESIDUE 1-220 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell: B-CELLS / Cell line: ANTI-NP MURINE HYBRIDOMA / Organ: SPLEEN / Strain: C57BL/6
#2: Antibody ANTI-NP MURINE GERMLINE MONOCLONAL ANTIBODY BBE6.12H3


Mass: 22538.885 Da / Num. of mol.: 1 / Fragment: ANTIGEN-BINDING FRAGMENT, RESIDUES 1-211 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell: B-CELLS / Cell line: ANTI-NP MURINE HYBRIDOMA / Organ: SPLEEN / Strain: C57BL/6
#3: Protein/peptide DODECAPEPTIDE (DLWTTAIPTIPS)


Mass: 1314.483 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.02 Å3/Da / Density % sol: 39.15 % / Description: NONE
Crystal growpH: 7.1
Details: 0.05M TRIS HCL, 0.025% SODIUM AZIDE, PEG 3350., pH 7.1

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9537
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 28, 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: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 11098 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.3
Reflection shellResolution: 2.7→8.5 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4.1 / % possible all: 100

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Processing

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

Resolution: 2.7→50 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1553445.18 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: IN CHAIN H, RESIDUES 136-140 COULD NOT BE MODELLED OWING TO MISSING ELECTRON DENSITY. IN CHAIN P, SIDECHAINS OF RESIDUES 9, 11, AND 12 COULD NOT BE MODELLED OWING TO MISSING ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2477 1081 9.7 %RANDOM
Rwork0.2305 ---
obs0.2305 9995 90.1 %-
Solvent computationSolvent model: FLAT / Bsol: 45.0508 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 42.4 Å2
Baniso -1Baniso -2Baniso -3
1--12.165 Å20 Å2-1.132 Å2
2--26.388 Å20 Å2
3----14.223 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3294 0 0 99 3393
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009918
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_deg1.96434
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_d1.3
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: 2.7→2.87 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.35 187 11.4 %
Rwork0.3 1456 -
obs--90.1 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR PROTEIN_REP.PARAM
X-RAY DIFFRACTION2CNS_TOPPAR WATER_REP.PARAM

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