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

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Basic information

Entry
Database: PDB / ID: 2xzq
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 YQLRPNAETLRF
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: 2.4 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
DepositionDec 1, 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 / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0485
Polymers47,9173
Non-polymers1312
Water2,270126
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-103.4 kcal/mol
Surface area19100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.920, 65.280, 113.560
Angle α, β, γ (deg.)90.00, 90.19, 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: 23683.525 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: 22724.068 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: 1509.708 Da / Num. of mol.: 1 / Fragment: PEPTIDE, RESIDUES 1-12 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.07 Å3/Da / Density % sol: 40.1 % / Description: NONE
Crystal growpH: 7.1
Details: 0.05 M TRIS HCL, 0.025% SODIUM AZIDE, PEG 3350., pH 7.1

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.953
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 29, 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: 0.953 Å / Relative weight: 1
ReflectionResolution: 2.4→39.82 Å / Num. obs: 16150 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.5
Reflection shellResolution: 2.4→6.9 Å / Redundancy: 6 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 7.9 / % possible all: 98.1

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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: 2.4→50 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2506 1572 9.7 %RANDOM
Rwork0.2407 ---
obs0.2407 16061 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.2946 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 28 Å2
Baniso -1Baniso -2Baniso -3
1-2.06 Å20 Å2-1.341 Å2
2--11.421 Å20 Å2
3----13.481 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3306 0 2 126 3434
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008176
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_deg1.81797
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d28.07
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.04
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: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.31 260 9.9 %
Rwork0.29 2366 -
obs--98.2 %
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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