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- PDB-4aeh: Crystal structure of the anti-AaHI Fab9C2 antibody -

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Basic information

Entry
Database: PDB / ID: 4aeh
TitleCrystal structure of the anti-AaHI Fab9C2 antibody
Components
  • FAB ANTIBODY, HEAVY CHAIN
  • FAB ANTIBODY, LIGHT CHAIN
KeywordsIMMUNE SYSTEM / ANDROCTONUS / ALPHA-TOXIN / COMBINING SITE / EPITOPE / PHARMACOLOGICAL SITE / VENOM / VOLTAGE- ACTIVATED SODIUM CHANNEL / SCORPION
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsFabrichny, I.P. / Mondielli, G. / Conrod, S. / Martin-Eauclaire, M.F. / Bourne, Y. / Marchot, P.
Citation
Journal: J.Biol.Chem. / Year: 2012
Title: Structural Insights Into Antibody Sequestering and Neutralizing of Na+-Channel & [Alpha]-Type Modulator from Old-World Scorpion Venom
Authors: Fabrichny, I.P. / Mondielli, G. / Conrod, S. / Martin-Eauclaire, M.F. / Bourne, Y. / Marchot, P.
#1: Journal: Eur.J.Biochem. / Year: 2001
Title: Construction and Functional Evaluation of a Single-Chain Antibody Fragment that Neutralizes Toxin Aahi from the Venom of the Scorpion Androctonus Australis Hector.
Authors: Devaux, C. / Moreau, E. / Goyffon, M. / Rochat, H. / Billiald, P.
History
DepositionJan 10, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1May 2, 2012Group: Other
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
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 / _pdbx_entry_details.has_protein_modification

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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


Theoretical massNumber of molelcules
Total (without water)48,2022
Polymers48,2022
Non-polymers00
Water11,061614
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-24.3 kcal/mol
Surface area19510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.930, 71.030, 65.960
Angle α, β, γ (deg.)90.00, 111.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody FAB ANTIBODY, HEAVY CHAIN


Mass: 24524.275 Da / Num. of mol.: 1 / Fragment: VARIABLE DOMAIN, RESIDUES 1-231 / Source method: isolated from a natural source / Details: IGG2A, K-ISSUED ANTIBODY / Source: (natural) MUS MUSCULUS (house mouse)
#2: Antibody FAB ANTIBODY, LIGHT CHAIN


Mass: 23678.111 Da / Num. of mol.: 1 / Fragment: VARIABLE DOMAIN, RESIDUES 1-214 / Source method: isolated from a natural source / Details: IGG2A, K-ISSUED ANTIBODY / Source: (natural) MUS MUSCULUS (house mouse)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 614 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSEE REFERENCE IN REMARK 1 FOR SEQUENCES OF CHAIN L AND CHAIN H.

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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: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growpH: 7
Details: 12.5% PEG 4000, 0.1 M IMIDAZOLE-MALATE PH 7.0, 50 MM NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9798
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.6→15 Å / Num. obs: 63057 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 37.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.26
Reflection shellResolution: 1.6→1.65 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.8 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.777 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT.
RfactorNum. reflection% reflectionSelection details
Rfree0.21359 3155 5 %RANDOM
Rwork0.17407 ---
obs0.17606 59927 99.68 %-
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: 22.612 Å2
Baniso -1Baniso -2Baniso -3
1-1.32 Å20 Å2-1.02 Å2
2---0.02 Å20 Å2
3----2.07 Å2
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3281 0 0 614 3895
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.023683
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.945072
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4495498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.00124.667150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.91515586
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5441515
X-RAY DIFFRACTIONr_chiral_restr0.0960.2560
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212893
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 226 -
Rwork0.285 4347 -
obs--99.89 %
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)
10.9328-0.3051-0.01570.6128-0.17580.37920.05030.03430.0241-0.04-0.0259-0.03360.0184-0.0105-0.02450.0158-0.0059-0.00060.00860.00360.0066-4.427812.5136-0.2723
20.6893-0.1042-0.12230.4782-0.0550.8089-0.0453-0.04490.02120.05840.0245-0.0522-0.03360.01450.02090.01380.0007-0.00380.0082-0.00640.01111.8033-1.449731.9856
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 107
2X-RAY DIFFRACTION1H1 - 119
3X-RAY DIFFRACTION2L108 - 211
4X-RAY DIFFRACTION2H120 - 219

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