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- PDB-4otx: Structure of the anti-Francisella tularensis O-antigen antibody N... -

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Basic information

Entry
Database: PDB / ID: 4otx
TitleStructure of the anti-Francisella tularensis O-antigen antibody N203 Fab fragment
Components
  • N203 heavy chain
  • N203 light chain
KeywordsIMMUNE SYSTEM / antibody / lipopolysaccharide / internal epitope
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / AZIDE ION
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsLu, Z. / Rynkiewicz, M.J. / Yang, C.-Y. / Madico, G. / Perkins, H.M. / Roche, M.I. / Seaton, B.A. / Sharon, J.
CitationJournal: Monoclon Antib Immunodiagn Immunother / Year: 2014
Title: Functional and Structural Characterization of Francisella tularensis O-Antigen Antibodies at the Low End of Antigen Reactivity.
Authors: Lu, Z. / Rynkiewicz, M.J. / Yang, C.Y. / Madico, G. / Perkins, H.M. / Roche, M.I. / Seaton, B.A. / Sharon, J.
History
DepositionFeb 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Sep 20, 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 2.2Oct 30, 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
L: N203 light chain
H: N203 heavy chain
M: N203 light chain
I: N203 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,90123
Polymers94,2214
Non-polymers68019
Water11,908661
1
L: N203 light chain
H: N203 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3238
Polymers47,1102
Non-polymers2136
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-68 kcal/mol
Surface area18960 Å2
MethodPISA
2
M: N203 light chain
I: N203 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,57815
Polymers47,1102
Non-polymers46713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-152 kcal/mol
Surface area19180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.011, 122.322, 124.764
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody N203 light chain


Mass: 24223.732 Da / Num. of mol.: 2 / Fragment: Fab / Source method: isolated from a natural source / Details: hybridoma / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C
#2: Antibody N203 heavy chain


Mass: 22886.566 Da / Num. of mol.: 2 / Fragment: Fab / Source method: isolated from a natural source / Details: hybridoma / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: N3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 661 / 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: 2.67 Å3/Da / Density % sol: 53.98 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4
Details: Crystals were grown by streak seeding into an overnight equilibrated drop containing 0.5 ul of Fab (38mg/ml) and 0.5 ul of reservoir solution [0.1 M sodium citrate (pH 4.0), 1 M lithium ...Details: Crystals were grown by streak seeding into an overnight equilibrated drop containing 0.5 ul of Fab (38mg/ml) and 0.5 ul of reservoir solution [0.1 M sodium citrate (pH 4.0), 1 M lithium chloride, 13-16% PEG 6000], VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→15 Å / Num. obs: 58890 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 27.28 Å2 / Rmerge(I) obs: 0.07 / Χ2: 1.455 / Net I/σ(I): 14.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.173.60.34956491.341196.3
2.17-2.263.90.358141.359199
2.26-2.363.80.25158371.413199.2
2.36-2.4940.20958611.38199.6
2.49-2.644.20.16158991.389199.8
2.64-2.854.20.11858821.446199.9
2.85-3.134.20.08159341.512199.9
3.13-3.584.20.05659431.566199.7
3.58-4.494.20.04159761.632199.3
4.49-154.10.03560951.463197.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.79 Å15 Å
Translation3.79 Å15 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.0phasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: the light chain of PDB code 1MCP and the heavy (H) chain of PDB code 3CLE

1mcp

3cle


Resolution: 2.1→14.857 Å / SU ML: 0.21 / σ(F): 0 / Phase error: 24.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2283 1928 3.38 %
Rwork0.1928 --
obs0.194 57003 95.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.74 Å2 / Biso mean: 28.0236 Å2 / Biso min: 7.87 Å2
Refinement stepCycle: LAST / Resolution: 2.1→14.857 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6452 0 21 661 7134
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026670
X-RAY DIFFRACTIONf_angle_d0.6749079
X-RAY DIFFRACTIONf_chiral_restr0.0451019
X-RAY DIFFRACTIONf_plane_restr0.0031149
X-RAY DIFFRACTIONf_dihedral_angle_d9.9532386
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0999-2.15230.26491240.21533409353384
2.1523-2.21030.26171250.21453710383591
2.2103-2.27510.27771390.21793795393493
2.2751-2.34830.27241270.21913803393094
2.3483-2.43190.29121330.22193875400895
2.4319-2.52880.26031340.22723892402696
2.5288-2.64330.27931410.21723962410397
2.6433-2.78180.26911420.22533981412398
2.7818-2.95480.26731420.21974009415198
2.9548-3.18080.27431350.22544086422199
3.1808-3.49720.2481470.19924094424199
3.4972-3.99460.19521450.17044099424499
3.9946-5.00070.15471420.14314149429199
5.0007-14.85750.17721520.16564211436397

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