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- PDB-3ujt: Structure of the Fab fragment of Ab-52, an antibody that binds th... -

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Basic information

Entry
Database: PDB / ID: 3ujt
TitleStructure of the Fab fragment of Ab-52, an antibody that binds the O-antigen of Francisella tularensis
Components
  • Ab-52 heavy chain
  • Ab-52 light chain
KeywordsIMMUNE SYSTEM / immunoglobulin / O-antigen
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRynkiewicz, M.J. / Lu, Z. / Hui, J.H. / Sharon, J. / Seaton, B.A.
CitationJournal: Biochemistry / Year: 2012
Title: Structural Analysis of a Protective Epitope of the Francisella tularensis O-Polysaccharide.
Authors: Rynkiewicz, M.J. / Lu, Z. / Hui, J.H. / Sharon, J. / Seaton, B.A.
History
DepositionNov 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Sep 13, 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
H: Ab-52 heavy chain
L: Ab-52 light chain
I: Ab-52 heavy chain
M: Ab-52 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,00211
Polymers93,2684
Non-polymers7357
Water14,484804
1
H: Ab-52 heavy chain
L: Ab-52 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0626
Polymers46,6342
Non-polymers4284
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-20 kcal/mol
Surface area19100 Å2
MethodPISA
2
I: Ab-52 heavy chain
M: Ab-52 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9405
Polymers46,6342
Non-polymers3063
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-19 kcal/mol
Surface area19140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.953, 131.491, 86.805
Angle α, β, γ (deg.)90.00, 96.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Ab-52 heavy chain


Mass: 22677.324 Da / Num. of mol.: 2 / Fragment: Fab fragment / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: hybridoma / Strain: BALB/c
#2: Antibody Ab-52 light chain


Mass: 23956.498 Da / Num. of mol.: 2 / Fragment: Fab fragment / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: hybridoma / Strain: BALB/c
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 804 / Source method: isolated from a natural source / Formula: H2O

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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: 2.18 Å3/Da / Density % sol: 43.69 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M tris, 24% w/v PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 9, 2010
RadiationMonochromator: Double Mirrors / Protocol: 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. all: 46183 / Num. obs: 46183 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Rmerge(I) obs: 0.075
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.337 / Num. unique all: 4572 / % possible all: 99.4

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIX(AutoMR)model building
PHENIX(phenix.refine: 1.6.3_473)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIX(AutoMR)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1RJL heavy chain, and PDB entry 3GI8 light chain

1rjl

3gi8


Resolution: 2.1→14.842 Å / SU ML: 0.27 / σ(F): 0 / Phase error: 22.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2196 1936 4.33 %RANDOM
Rwork0.1858 ---
obs0.1873 44718 96.07 %-
all-46183 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.739 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.1438 Å20 Å20.3408 Å2
2--0.5585 Å2-0 Å2
3----1.7023 Å2
Refinement stepCycle: LAST / Resolution: 2.1→14.842 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6480 0 48 804 7332
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026685
X-RAY DIFFRACTIONf_angle_d0.6229083
X-RAY DIFFRACTIONf_dihedral_angle_d12.4882375
X-RAY DIFFRACTIONf_chiral_restr0.0411028
X-RAY DIFFRACTIONf_plane_restr0.0031144
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.17370.28741780.22183949X-RAY DIFFRACTION90
2.1737-2.26040.31051930.22014191X-RAY DIFFRACTION94
2.2604-2.36290.27511930.21584184X-RAY DIFFRACTION94
2.3629-2.48690.26161900.2154215X-RAY DIFFRACTION95
2.4869-2.64190.27251900.20674314X-RAY DIFFRACTION97
2.6419-2.84460.23041930.20374299X-RAY DIFFRACTION97
2.8446-3.12850.241960.19054332X-RAY DIFFRACTION98
3.1285-3.57560.20552000.17454429X-RAY DIFFRACTION99
3.5756-4.48420.1632010.15134441X-RAY DIFFRACTION99
4.4842-14.8420.17072020.16744428X-RAY DIFFRACTION99

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