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- PDB-2v17: Structure of the complex of antibody MN423 with a fragment of tau... -

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Basic information

Entry
Database: PDB / ID: 2v17
TitleStructure of the complex of antibody MN423 with a fragment of tau protein
Components
  • (MONOCLONAL ANTIBODY FAB FRAGMENT MN423) x 2
  • PEPTIDE FRAGMENT
KeywordsIMMUNE SYSTEM / MICROTUBULE / TAU PROTEIN / ALZHEIMER'S DISEASE
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHOMO SAPIENS (human)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSevcik, J. / Skrabana, R. / Csokova, N. / Dvorsky, R. / Novak, M.
CitationJournal: FEBS Lett. / Year: 2007
Title: X-Ray Structure of the Phf Core C-Terminus: Insight Into the Folding of the Intrinsically Disordered Protein Tau in Alzheimer'S Disease.
Authors: Sevcik, J. / Skrabana, R. / Dvorsky, R. / Csokova, N. / Iqbal, K. / Novak, M.
History
DepositionMay 22, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 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 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PEPTIDE FRAGMENT
H: MONOCLONAL ANTIBODY FAB FRAGMENT MN423
L: MONOCLONAL ANTIBODY FAB FRAGMENT MN423


Theoretical massNumber of molelcules
Total (without water)47,9053
Polymers47,9053
Non-polymers00
Water12,647702
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-39.6 kcal/mol
Surface area23670 Å2
MethodPQS
Unit cell
Length a, b, c (Å)71.541, 36.808, 85.543
Angle α, β, γ (deg.)90.00, 113.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide PEPTIDE FRAGMENT


Mass: 629.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell: B-LYMPHOCYTE / Cell line: MN423 HYBRIDOMA / Organ: SPLEEN
#2: Antibody MONOCLONAL ANTIBODY FAB FRAGMENT MN423


Mass: 23496.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DISULPHIDE BRIDGE BETWEEN L214 AND H137 IS REDUCED / Source: (natural) MUS MUSCULUS (house mouse) / Cell: B-LYMPHOCYTE / Cell line: MN423 HYBRIDOMA / Organ: SPLEEN
#3: Antibody MONOCLONAL ANTIBODY FAB FRAGMENT MN423


Mass: 23779.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DISULPHIDE BRIDGE BETWEEN L214 AND H137 IS REDUCED / Source: (natural) MUS MUSCULUS (house mouse) / Cell: B-LYMPHOCYTE / Cell line: MN423 HYBRIDOMA / Organ: SPLEEN
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 702 / 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: 2.3 Å3/Da / Density % sol: 45.8 % / Description: NONE
Crystal growpH: 7.5
Details: CRYSTALS WERE GROWN FROM 3 UL DROPS CONTAINING 10MG/ML OF PROTEIN, 15 % PEG1000, 100MM HEPES, PH 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8423
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 10, 2006 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8423 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. obs: 49464 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 20.1
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.7 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NBV

1nbv


Resolution: 1.65→79.06 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.932 / SU B: 1.805 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THREE C-TERMINAL RESIDUES IN HEAVY CHAIN WERE NOT DETERMINED
RfactorNum. reflection% reflectionSelection details
Rfree0.218 2504 5.1 %RANDOM
Rwork0.156 ---
obs0.16 46957 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20.2 Å2
2--0.15 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.65→79.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3365 0 0 702 4067
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0213455
X-RAY DIFFRACTIONr_bond_other_d0.0030.022971
X-RAY DIFFRACTIONr_angle_refined_deg1.6631.954705
X-RAY DIFFRACTIONr_angle_other_deg1.21736965
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.095439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1820.2527
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023853
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02691
X-RAY DIFFRACTIONr_nbd_refined0.2520.2710
X-RAY DIFFRACTIONr_nbd_other0.270.23771
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0880.22069
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2220.2486
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2620.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3390.297
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1930.283
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3111.52199
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.21823553
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.93731252
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2674.51142
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: 1.65→1.69 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.223 192
Rwork0.15 3413

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