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- PDB-5mx3: Structure of DC8E8 Fab crystallized at pH 8.5 -

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Basic information

Entry
Database: PDB / ID: 5mx3
TitleStructure of DC8E8 Fab crystallized at pH 8.5
Components
  • antibody Fab heavy chain
  • antibody kappa chain
KeywordsIMMUNE SYSTEM / Fab
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.98 Å
AuthorsSkrabana, R. / Novak, M. / Cehlar, O. / Kontsekova, E.
Citation
Journal: To be published
Title: Structure of DC8E8 Fab crystallized at pH 8.5
Authors: Skrabana, R.
#1: Journal: Alzheimers Res Ther / Year: 2014
Title: Identification of structural determinants on tau protein essential for its pathological function: novel therapeutic target for tau immunotherapy in Alzheimer's disease.
Authors: Kontsekova, E. / Zilka, N. / Kovacech, B. / Skrabana, R. / Novak, M.
History
DepositionJan 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_id_ISSN / _citation.page_last
SupersessionMar 11, 2020ID: 4OZ4
Revision 2.0Mar 11, 2020Group: Advisory / Polymer sequence / Category: entity_poly / pdbx_database_PDB_obs_spr / Item: _entity_poly.pdbx_seq_one_letter_code_can
Revision 2.1Jan 17, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: antibody Fab heavy chain
L: antibody kappa chain
A: antibody Fab heavy chain
B: antibody kappa chain


Theoretical massNumber of molelcules
Total (without water)95,7174
Polymers95,7174
Non-polymers00
Water0
1
H: antibody Fab heavy chain
L: antibody kappa chain


Theoretical massNumber of molelcules
Total (without water)47,8582
Polymers47,8582
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-22 kcal/mol
Surface area19370 Å2
MethodPISA
2
A: antibody Fab heavy chain
B: antibody kappa chain


Theoretical massNumber of molelcules
Total (without water)47,8582
Polymers47,8582
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-22 kcal/mol
Surface area19450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.110, 111.030, 95.860
Angle α, β, γ (deg.)90.000, 90.380, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody antibody Fab heavy chain


Mass: 23685.529 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody antibody kappa chain


Mass: 24172.787 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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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: 2.29 Å3/Da / Density % sol: 46.18 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 30% PEG 4000, 0.1 M Tris, 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 28, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.755
11-h,-k,l20.245
ReflectionResolution: 2.98→37.87 Å / Num. obs: 14700 / % possible obs: 83.2 % / Observed criterion σ(I): -3 / Redundancy: 2.376 % / Biso Wilson estimate: 48.032 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.121 / Rrim(I) all: 0.154 / Χ2: 0.955 / Net I/σ(I): 8.26
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.98-3.062.2760.5111.9411100.7760.65385.5
3.06-3.142.310.4142.4211080.8590.52686.6
3.14-3.232.3280.3542.910410.8570.45185.3
3.23-3.332.3590.3363.0710100.8880.42684.8
3.33-3.442.3060.2514.19960.9290.32284.8
3.44-3.562.3690.1965.599190.960.2583.5
3.56-3.72.3480.1816.129400.950.23184.5
3.7-3.852.3670.1826.088640.9460.23483.5
3.85-4.022.3820.167.288230.9640.20582.1
4.02-4.212.3890.129.47960.9750.15483.3
4.21-4.442.4190.09510.777520.9860.12182.8
4.44-4.712.4160.08412.447160.9870.10782.7
4.71-5.042.430.08512.656790.990.10882
5.04-5.442.4340.07313.486060.9910.09381.9
5.44-5.962.4490.08711.665730.9860.11280.9
5.96-6.662.5320.08912.15020.9880.11379.7
6.66-7.692.4740.05915.764430.9930.07579.7
7.69-9.422.4880.03223.83750.9980.04278.8
9.42-13.332.3960.02332.422980.9990.02978.8
13.33-37.872.4030.02331.371490.9990.02972

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OZ4

4oz4
PDB Unreleased entry


Resolution: 2.98→37.87 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.87 / SU B: 19.563 / SU ML: 0.359 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.123
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2559 703 4.9 %RANDOM
Rwork0.2186 ---
obs0.2203 13690 81.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 162.11 Å2 / Biso mean: 59.906 Å2 / Biso min: 21.53 Å2
Baniso -1Baniso -2Baniso -3
1-61.29 Å20 Å2-5.16 Å2
2---26.53 Å2-0 Å2
3----34.76 Å2
Refinement stepCycle: final / Resolution: 2.98→37.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6680 0 0 0 6680
Num. residues----876
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.026852
X-RAY DIFFRACTIONr_bond_other_d0.0030.026067
X-RAY DIFFRACTIONr_angle_refined_deg1.4781.9479323
X-RAY DIFFRACTIONr_angle_other_deg1.032314175
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7925872
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.56624.208259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.272151093
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1191525
X-RAY DIFFRACTIONr_chiral_restr0.0770.21048
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217571
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021374
LS refinement shellResolution: 2.98→3.058 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 25 -
Rwork0.314 788 -
all-813 -
obs--62.93 %

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