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- PDB-4bh8: CRYSTAL STRUCTURE OF GERMLINE ANTIBODY 36-65 IN COMPLEX WITH PEPT... -

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Basic information

Entry
Database: PDB / ID: 4bh8
TitleCRYSTAL STRUCTURE OF GERMLINE ANTIBODY 36-65 IN COMPLEX WITH PEPTIDE GDPRPSYISHLL
Components
  • (ANTI-ARS MURINE GERMLINE MONOCLONAL ANTIBODY 36-65) x 2
  • DODECAPEPTIDE ANTIGEN
KeywordsIMMUNE SYSTEM / GERMLINE ANTIBODY / ANTIBODY POLYSPECIFICTY
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: 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 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
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)48,9623
Polymers48,9623
Non-polymers00
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-45.2 kcal/mol
Surface area24360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.410, 76.970, 59.260
Angle α, β, γ (deg.)90.00, 101.74, 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: 23663.084 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: 1356.528 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.: 190 / 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: 2.43 Å3/Da / Density % sol: 49.4 % / Description: NO
Crystal growpH: 6.7 / Details: 0.05 M SODIUM CACODYLATE, PH 6.7, 21% PEG

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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: Apr 9, 2009 / 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: 2.4→58 Å / Num. obs: 19076 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.2refinement
MOSFLMdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2A6J

2a6j


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
Rfree0.251 1842 9.8 %RANDOM
Rwork0.2305 ---
obs0.2305 18818 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 21.262 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 31 Å2
Baniso -1Baniso -2Baniso -3
1--2.042 Å20 Å2-1.607 Å2
2--3.742 Å20 Å2
3----1.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3379 0 0 190 3569
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007262
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_deg1.69316
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.06
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: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.35 291 9.8 %
Rwork0.34 2664 -
obs--94.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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