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- PDB-4bh7: CRYSTAL STRUCTURE OF GERMLINE ANTIBODY 36-65 IN COMPLEX WITH PEPT... -

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Basic information

Entry
Database: PDB / ID: 4bh7
TitleCRYSTAL STRUCTURE OF GERMLINE ANTIBODY 36-65 IN COMPLEX WITH PEPTIDE PPYPAWHAPGNI
Components
  • (ANTI-ARS MURINE GERMLINE MONOCLONAL ANTIBODY 36-65) x 2
  • DODECAPEPTIDE ANTIGEN
KeywordsIMMUNE SYSTEM / CONVERGENCE OF ANTIBODY SPECIFICITIES
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: 2.89 Å
AuthorsKhan, T. / Salunke, D.M.
CitationJournal: J.Immunol. / Year: 2014
Title: Adjustable Locks and Flexible Keys: Plasticity of Epitope-Paratope Interactions in Germline Antibodies.
Authors: Khan, T. / Salunke, D.M.
History
DepositionMar 30, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references
Revision 1.2May 28, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: 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 1.4Nov 20, 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
A: ANTI-ARS MURINE GERMLINE MONOCLONAL ANTIBODY 36-65
B: ANTI-ARS MURINE GERMLINE MONOCLONAL ANTIBODY 36-65
P: DODECAPEPTIDE ANTIGEN


Theoretical massNumber of molelcules
Total (without water)48,8843
Polymers48,8843
Non-polymers00
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-42.1 kcal/mol
Surface area24140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.560, 76.770, 59.170
Angle α, β, γ (deg.)90.00, 102.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody ANTI-ARS MURINE GERMLINE MONOCLONAL ANTIBODY 36-65


Mass: 23620.893 Da / Num. of mol.: 1 / Fragment: ANTIGEN BINDING FRAGMENT / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell: B CELL / Cell line: 36-65 HYBRIDOMA / Organ: SPLEEN / Strain: BALB/C
#2: Antibody ANTI-ARS MURINE GERMLINE MONOCLONAL ANTIBODY 36-65


Mass: 23942.768 Da / Num. of mol.: 1 / Fragment: ANTIGEN BINDING FRAGMENT / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell: B CELL / Cell line: 36-65 HYBRIDOMA / Organ: SPLEEN / Strain: BALB/C
#3: Protein/peptide DODECAPEPTIDE ANTIGEN


Mass: 1320.473 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.4 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.05 M SODIUM CACODYLATE PH 6.5, 18% PEG 3000

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 13, 2006 / Details: MIRRORS
RadiationMonochromator: NI FILTER CMF12 38CU-6 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.89→57 Å / Num. obs: 10548 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.4
Reflection shellResolution: 2.89→3.05 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.9 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2A6J

2a6j


Resolution: 2.89→57.81 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.886 / SU B: 15.702 / SU ML: 0.262 / Cross valid method: THROUGHOUT / ESU R Free: 0.325 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.25419 1034 9.8 %RANDOM
Rwork0.22733 ---
obs0.22993 9490 97.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.643 Å2
Baniso -1Baniso -2Baniso -3
1--1.04 Å20 Å2-1.09 Å2
2--1.4 Å20 Å2
3----0.83 Å2
Refinement stepCycle: LAST / Resolution: 2.89→57.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3381 0 0 77 3458
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223467
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8041.9494723
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3825436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.4224.113141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.68415544
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.7591515
X-RAY DIFFRACTIONr_chiral_restr0.1360.2524
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212634
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9161.52190
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.68523553
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.47331277
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4054.51170
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.89→2.965 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 77 -
Rwork0.322 717 -
obs--100 %

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