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- PDB-2y07: CRYSTAL STRUCTURE ANALYSIS OF THE ANTI-(4-HYDROXY-3-NITROPHENYL) ... -

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Basic information

Entry
Database: PDB / ID: 2y07
TitleCRYSTAL STRUCTURE ANALYSIS OF THE ANTI-(4-HYDROXY-3-NITROPHENYL) - ACETYL MURINE GERMLINE MONOCLONAL ANTIBODY BBE6.12H3 FAB FRAGMENT IN COMPLEX WITH A PHAGE DISPLAY DERIVED DODECAPEPTIDE PPYPAWHAPGNI
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 / MOLECULAR REPLACEMENT / Resolution: 2.4 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 1.2May 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)47,3173
Polymers47,3173
Non-polymers00
Water2,684149
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-33.1 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.359, 60.829, 111.724
Angle α, β, γ (deg.)90.00, 94.79, 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: 22538.818 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: 1320.473 Da / Num. of mol.: 1 / Fragment: PEPTIDE, RESIDUES 1-12 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 1.84 Å3/Da / Density % sol: 33.2 % / Description: NONE
Crystal growpH: 7.1
Details: 50 MM TRIS HCL, 0.025% SODIUM AZIDE, PEG 3350, pH 7.1

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 30, 2008 / Details: MIRRORS
RadiationMonochromator: NI FILTER CMF12 38CU-6 (OSMIC INC.) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→23.62 Å / Num. obs: 14326 / % possible obs: 95.5 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 5
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 3 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 3.6 / % possible all: 93.6

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Processing

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

Resolution: 2.4→23.62 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 184279.07 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2572 1310 9.1 %RANDOM
Rwork0.2344 ---
obs0.2344 13136 91.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 25.8733 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 37 Å2
Baniso -1Baniso -2Baniso -3
1-3.95 Å20 Å27.569 Å2
2--7.319 Å20 Å2
3----11.268 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.4→23.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3256 0 0 149 3405
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009093
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_deg1.7825
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.7
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: 2.4→2.55 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.34 197 9.6 %
Rwork0.33 1859 -
obs--86.6 %
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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