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- PDB-4tpr: Structure of Tau5 antibody Fab fragment -

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Basic information

Entry
Database: PDB / ID: 4tpr
TitleStructure of Tau5 antibody Fab fragment
Components
  • Fab heavy chain
  • If kappa light chain
KeywordsIMMUNE SYSTEM / monoclonal antibody
Function / homology
Function and homology information


: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-33O / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / If kappa light chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsCehlar, O. / Skrabana, R. / Novak, M.
CitationJournal: To Be Published
Title: Structure of Tau5 antibody Fab fragment
Authors: Cehlar, O. / Skrabana, R. / Novak, M.
History
DepositionJun 9, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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
L: If kappa light chain
H: Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,87318
Polymers47,8902
Non-polymers1,98216
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7320 Å2
ΔGint-38 kcal/mol
Surface area19770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.374, 50.408, 75.169
Angle α, β, γ (deg.)90.00, 115.35, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11L-303-

CL

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Components

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Antibody , 2 types, 2 molecules LH

#1: Antibody If kappa light chain / Fab light chain


Mass: 24102.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: A2NHM3
#2: Antibody Fab heavy chain


Mass: 23787.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Non-polymers , 8 types, 359 molecules

#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#9: Chemical ChemComp-33O / 3,6,9,12,15,18,21,24,27,30,33,36-dodecaoxaoctatriacontane-1,38-diol / Tridecaethyleneglycol


Mass: 590.699 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H54O14
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.2 M NaCl, 0.1 M Bis-Tris, 25 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.97004 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97004 Å / Relative weight: 1
ReflectionResolution: 1.6→67.93 Å / Num. obs: 54464 / % possible obs: 93.9 % / Redundancy: 7.236 % / Rmerge(I) obs: 0.156 / Net I/σ(I): 10.64
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 6.69 % / Rmerge(I) obs: 1.6 / Mean I/σ(I) obs: 1.22 / % possible all: 64.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementStarting model: 1200000000 / Resolution: 1.6→67.93 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.546 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19109 2736 5 %RANDOM
Rwork0.14259 ---
obs0.14502 51747 94.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.284 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å2-0.21 Å2
2---0.02 Å2-0 Å2
3---0.43 Å2
Refinement stepCycle: 1 / Resolution: 1.6→67.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3369 0 125 343 3837
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.023791
X-RAY DIFFRACTIONr_bond_other_d0.0020.023455
X-RAY DIFFRACTIONr_angle_refined_deg1.3641.9615170
X-RAY DIFFRACTIONr_angle_other_deg0.75138053
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3245495
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.07324.497149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.84115586
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5471514
X-RAY DIFFRACTIONr_chiral_restr0.0840.2560
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214313
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02849
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_it1.9121.5631867
X-RAY DIFFRACTIONr_mcbond_other1.9091.5591865
X-RAY DIFFRACTIONr_mcangle_it2.5082.342363
X-RAY DIFFRACTIONr_mcangle_other2.5082.3412364
X-RAY DIFFRACTIONr_scbond_it2.5911.9411924
X-RAY DIFFRACTIONr_scbond_other2.5861.9411924
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.992.7542796
X-RAY DIFFRACTIONr_long_range_B_refined4.08914.1944244
X-RAY DIFFRACTIONr_long_range_B_other4.08914.2034245
X-RAY DIFFRACTIONr_rigid_bond_restr3.05937245
X-RAY DIFFRACTIONr_sphericity_free31.6985128
X-RAY DIFFRACTIONr_sphericity_bonded8.52757351
LS refinement shellResolution: 1.601→1.643 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 138 -
Rwork0.299 2595 -
obs--64.44 %

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