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- PDB-2z93: Crystal structure of Fab fragment of anti-ciguatoxin antibody 10C... -

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Basic information

Entry
Database: PDB / ID: 2z93
TitleCrystal structure of Fab fragment of anti-ciguatoxin antibody 10C9 in complex with CTX3C-ABCD
Components
  • Anti-ciguatoxin antibody 10C9 Fab heavy chain
  • Anti-ciguatoxin antibody 10C9 Fab light chain
KeywordsIMMUNE SYSTEM / Immunogloburin like fold
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-END
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsUi, M. / Tanaka, Y. / Tsumoto, K.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: How Protein Recognizes Ladder-like Polycyclic Ethers: INTERACTIONS BETWEEN CIGUATOXIN (CTX3C) FRAGMENTS AND ITS SPECIFIC ANTIBODY 10C9
Authors: Ui, M. / Tanaka, Y. / Tsumuraya, T. / Fujii, I. / Inoue, M. / Hirama, M. / Tsumoto, K.
History
DepositionSep 14, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Anti-ciguatoxin antibody 10C9 Fab heavy chain
B: Anti-ciguatoxin antibody 10C9 Fab light chain
C: Anti-ciguatoxin antibody 10C9 Fab heavy chain
D: Anti-ciguatoxin antibody 10C9 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,4635
Polymers94,1224
Non-polymers3401
Water2,180121
1
A: Anti-ciguatoxin antibody 10C9 Fab heavy chain
B: Anti-ciguatoxin antibody 10C9 Fab light chain


Theoretical massNumber of molelcules
Total (without water)47,0612
Polymers47,0612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-13.2 kcal/mol
Surface area8760 Å2
MethodPISA
2
C: Anti-ciguatoxin antibody 10C9 Fab heavy chain
D: Anti-ciguatoxin antibody 10C9 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4013
Polymers47,0612
Non-polymers3401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-25.4 kcal/mol
Surface area17320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.725, 45.410, 122.371
Angle α, β, γ (deg.)90.00, 98.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Anti-ciguatoxin antibody 10C9 Fab heavy chain


Mass: 23837.537 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line: Hybridoma
#2: Antibody Anti-ciguatoxin antibody 10C9 Fab light chain


Mass: 23223.561 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line: Hybridoma
#3: Chemical ChemComp-END / 1,6:5,9:8,12:11,16-TETRAANHYDRO-2,3,4,10,13,14-HEXADEOXY-D-GLYCERO-D-ALLO-D-GULO-HEPTADECA-2,13-DIENITOL


Mass: 340.368 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H24O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS SEQUENCE HAS BEEN ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS SEQUENCE HAS BEEN DEPOSITED IN THE SEQUENCE DATABASE.

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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: 2.35 Å3/Da / Density % sol: 47.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M sodium acetate, 0.2M ammonium sulfate, 30% PEG MME 2000, pH4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 35513 / % possible obs: 99.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 36.1 Å2 / Rsym value: 0.056
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.1 % / Num. unique all: 3332 / Rsym value: 0.349 / % possible all: 94.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Z92

2z92


Resolution: 2.4→9.99 Å / Cor.coef. Fo:Fc: 0.877 / Cor.coef. Fo:Fc free: 0.822 / Rfactor Rfree error: 0.006 / SU B: 17.54 / SU ML: 0.21 / Data cutoff high absF: 1384755.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.372 / ESU R Free: 0.306 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.34 3396 9.9 %RANDOM
Rwork0.297 ---
obs-34177 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT MODEL / Bsol: 44.1197 Å2 / ksol: 0.414504 e/Å3
Displacement parametersBiso mean: 41.9 Å2
Baniso -1Baniso -2Baniso -3
1--15.59 Å20 Å21.87 Å2
2--19.23 Å20 Å2
3----3.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.4→9.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4162 0 24 121 4307
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.03
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_mcangle_it2.142
X-RAY DIFFRACTIONc_scbond_it1.92
X-RAY DIFFRACTIONc_scangle_it2.422.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.363 545 9.8 %
Rwork0.311 4992 -
obs--97.7 %
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)
15.82210.8706-0.59118.6004-2.07534.54060.15481.4226-0.9198-0.3432-0.14530.25660.40870.4754-0.0095-0.16630.0436-0.00060.5017-0.2565-0.279324.761-0.17829.685
26.0933-1.14980.89160.23570.073.9782-0.05791.1611-0.52810.00590.1538-0.07840.3830.0742-0.0959-0.0827-0.02310.05480.1-0.1282-0.13589.0061.97135.727
31.6611-0.4217-0.23881.8128-0.18881.0049-0.0930.1675-0.11820.01820.07230.01090.0663-0.2890.0207-0.1335-0.0190.0028-0.0788-0.0168-0.085843.421-6.47658.858
411.4637-0.2517-0.8160.0719-0.58555.5444-0.17812.1120.62060.12740.09220.0816-0.10670.03070.0859-0.31120.0528-0.03550.38160.2058-0.262147.2759.35831.67
51.89060.42-0.52070.5813-0.35981.8064-0.0072-0.01780.0885-0.0014-0.015-0.0967-0.0249-0.06960.0223-0.0750.01070.0325-0.20720.0016-0.038564.954-0.99460.022
67.82770.05622.63732.7277-1.30983.2993-0.55460.81460.9901-0.18090.3980.2476-0.3788-0.180.1567-0.084-0.0276-0.07940.05530.3351-0.082759.77518.86735.922
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A116 - 212
2X-RAY DIFFRACTION2B115 - 212
3X-RAY DIFFRACTION3C3 - 111
4X-RAY DIFFRACTION4C116 - 213
5X-RAY DIFFRACTION5D1 - 106
6X-RAY DIFFRACTION6D107 - 205
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3DFOBS:CTOX.paramDFOBS:CTOX.top

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