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- PDB-2e27: Crystal structure of Fv fragment of anti-ciguatoxin antibody comp... -

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Basic information

Entry
Database: PDB / ID: 2.0E+27
TitleCrystal structure of Fv fragment of anti-ciguatoxin antibody complexed with ABC-ring of ciguatoxin
Components(anti-ciguatoxin antibody, ...) x 2
KeywordsIMMUNE SYSTEM / Immunoglobulin fold
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-AB0
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsYokota, A. / Tanaka, Y. / Tsumoto, K.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Critical contribution of aromatic rings to specific recognition of polyether rings. The case of ciguatoxin CTX3C-ABC and its specific antibody 1C49.
Authors: Tsumoto, K. / Yokota, A. / Tanaka, Y. / Ui, M. / Tsumuraya, T. / Fujii, I. / Kumagai, I. / Nagumo, Y. / Oguri, H. / Inoue, M. / Hirama, M.
History
DepositionNov 8, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE A sequence database reference for this protein does not currently exist. The SEQRES of ...SEQUENCE A sequence database reference for this protein does not currently exist. The SEQRES of chain L includes His tags(AAGHHHHHH) on the C-terminus. The SEQRES of chain H includes His tags(SAGHHHHHH) on the C-terminus. The residue numbering of chain H corresponds to Kabat database in which the residue numbers of antibody are defined. The residues in variable region are assigned with non-sequencial number.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: anti-ciguatoxin antibody, light chain
H: anti-ciguatoxin antibody, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,83810
Polymers26,8772
Non-polymers9618
Water2,990166
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.219, 97.502, 115.722
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

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Antibody , 2 types, 2 molecules LH

#1: Antibody anti-ciguatoxin antibody, light chain


Mass: 13190.817 Da / Num. of mol.: 1 / Fragment: Fv fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pARA7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Antibody anti-ciguatoxin antibody, heavy chain


Mass: 13686.045 Da / Num. of mol.: 1 / Fragment: Fv fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pARA7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)

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Non-polymers , 4 types, 174 molecules

#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-AB0 / 3,7:6,10:9,14-TRIANHYDRO-2,5,11,12,13-PENTADEOXY-4-O-(METHOXYMETHYL)-L-ARABINO-L-ALLO-TETRADEC-12-ENONIC ACID / CIGUATOXIN ABC RING FRAGMENT


Mass: 344.357 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H24O8
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 25% polyethylene glycol monomethyl ether 5000, 0.2M ammonium sulfate, 0.1M MES, 4.7% dimethylsulfoxide, 15% glycerol, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 14, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. obs: 29463 / % possible obs: 98.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.058
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 9.6 / Num. unique all: 4082 / % possible all: 95.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AXS, 1FJ1

1axs

1fj1


Resolution: 1.7→19.72 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1640100.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1499 5.1 %RANDOM
Rwork0.198 ---
obs0.198 29447 98.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.7375 Å2 / ksol: 0.441356 e/Å3
Displacement parametersBiso mean: 20.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2--5.6 Å20 Å2
3----5.72 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.03 Å
Refinement stepCycle: LAST / Resolution: 1.7→19.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1713 0 62 166 1941
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.151.5
X-RAY DIFFRACTIONc_mcangle_it1.832
X-RAY DIFFRACTIONc_scbond_it2.132
X-RAY DIFFRACTIONc_scangle_it3.112.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.249 236 5 %
Rwork0.207 4481 -
obs--96.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2DFOBS:ligand.paramwater.top
X-RAY DIFFRACTION3water_rep.paramDFOBS:ligand.top

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