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- PDB-2ymx: Crystal structure of inhibitory anti-AChE Fab408 -

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Basic information

Entry
Database: PDB / ID: 2ymx
TitleCrystal structure of inhibitory anti-AChE Fab408
Components
  • FAB ANTIBODY HEAVY CHAIN
  • FAB ANTIBODY LIGHT CHAIN
KeywordsIMMUNE SYSTEM / ACETYLCHOLINESTERASE / INHIBITION / BACK DOOR REGION
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBourne, Y. / Renault, L. / Essono, S. / Mondielli, G. / Lamourette, P. / Bocquet, D. / Grassi, J. / Marchot, P.
CitationJournal: Plos One / Year: 2013
Title: Molecular Characterization of Monoclonal Antibodies that Inhibit Acetylcholinesterase by Targeting the Peripheral Site and Backdoor Region
Authors: Bourne, Y. / Renault, L. / Essono, S. / Mondielli, G. / Lamourette, P. / Boquet, D. / Grassi, J. / Marchot, P.
History
DepositionOct 10, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Aug 9, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 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
H: FAB ANTIBODY HEAVY CHAIN
L: FAB ANTIBODY LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7993
Polymers47,7072
Non-polymers921
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-26.1 kcal/mol
Surface area19830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.950, 129.111, 99.264
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11H-2004-

HOH

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Components

#1: Antibody FAB ANTIBODY HEAVY CHAIN


Mass: 24132.043 Da / Num. of mol.: 1 / Fragment: VARIABLE DOMAIN / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse)
#2: Antibody FAB ANTIBODY LIGHT CHAIN


Mass: 23574.840 Da / Num. of mol.: 1 / Fragment: VARIABLE DOMAIN / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.38 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growpH: 6 / Details: 18% PEG 6000, 100 MM SODIUM CACODYLATE PH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 13, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 35565 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 15
Reflection shellResolution: 1.9→2 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 3.8 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1FGV AND 1WEJ

1fgv

1wej


Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / SU B: 9.748 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES WITH TLS ADDED. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25353 732 2.1 %RANDOM
Rwork0.20845 ---
obs0.20937 34833 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.697 Å2
Baniso -1Baniso -2Baniso -3
1-1.38 Å20 Å20 Å2
2--1.01 Å20 Å2
3----2.39 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3320 0 6 212 3538
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.023420
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3471.9464674
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5145436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.68724.697132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.22315536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6841511
X-RAY DIFFRACTIONr_chiral_restr0.0890.2536
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212566
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_it1.0911.8451741
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8712.7542172
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.3371.9521678
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.2516.2135177
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 62 -
Rwork0.282 2382 -
obs--93.96 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.13850.3447-0.59552.8641.04962.2047-0.3236-0.0323-0.22420.18950.21960.15720.7599-0.04760.10390.3216-0.01690.07330.16910.05550.112922.488812.019335.6524
20.2475-0.258-0.05455.09730.71281.3998-0.01180.2416-0.1464-0.2232-0.0850.1616-0.0936-0.25220.09680.0187-0.0048-0.01760.2885-0.13170.167310.874117.7853.0512
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 108
2X-RAY DIFFRACTION1H1 - 124
3X-RAY DIFFRACTION2L109 - 212
4X-RAY DIFFRACTION2H125 - 224

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