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- PDB-4pb0: Structure of the Fab fragment of the anti-Francisella tularensis ... -

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Basic information

Entry
Database: PDB / ID: 4pb0
TitleStructure of the Fab fragment of the anti-Francisella tularensis GroEL antibody Ab53
Components
  • Ab53 heavy chain
  • Ab53 light chain
KeywordsIMMUNE SYSTEM / antibody
Function / homology
Function and homology information


Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsLu, Z. / Rynkiewicz, M.J. / Seaton, B.A. / Sharon, J.
CitationJournal: Plos One / Year: 2014
Title: B-Cell Epitopes in GroEL of Francisella tularensis.
Authors: Lu, Z. / Rynkiewicz, M.J. / Madico, G. / Li, S. / Yang, C.Y. / Perkins, H.M. / Sompuram, S.R. / Kodela, V. / Liu, T. / Morris, T. / Wang, D. / Roche, M.I. / Seaton, B.A. / Sharon, J.
History
DepositionApr 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 7, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_nat / pdbx_database_status ...entity_src_nat / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software
Item: _entity_src_nat.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible ..._entity_src_nat.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Ab53 heavy chain
L: Ab53 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,00311
Polymers47,4762
Non-polymers5279
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-99 kcal/mol
Surface area19680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.817, 151.817, 102.766
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11L-309-

HOH

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Components

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Antibody , 2 types, 2 molecules HL

#1: Antibody Ab53 heavy chain


Mass: 23771.576 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: spleen / Plasmid details: hybridoma / Strain: BALB/cJ / References: UniProt: Q6PIP8*PLUS
#2: Antibody Ab53 light chain


Mass: 23704.303 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: spleen / Plasmid details: hybridoma / Strain: BALB/cJ

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Non-polymers , 4 types, 195 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 3.6 Å3/Da / Density % sol: 65.84 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Ab53 (30 mg/ml in 20 mM Tris pH 7.5, 0.15 M NaCl, and 0.02% NaN3) was mixed with the Index Screen HT reagent A4 (2 M ammonium sulfate, 0.1 M bistris, pH 6.5) in sitting drops at 17C.

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→15 Å / Num. obs: 23646 / % possible obs: 96.3 % / Redundancy: 6.6 % / Biso Wilson estimate: 28.66 Å2 / Rmerge(I) obs: 0.089 / Χ2: 1.4 / Net I/av σ(I): 21.821 / Net I/σ(I): 13.5 / Num. measured all: 155055
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.5-2.595.90.37123161.3796.1
2.59-2.695.90.33122911.45395.4
2.69-2.816.10.25622801.45594.4
2.81-2.966.70.19922671.34393.8
2.96-3.146.60.1523131.32895.7
3.14-3.396.60.10323901.41198.2
3.39-3.7270.07124191.26598.6
3.72-4.256.90.05824211.3398.2
4.25-5.3170.04824411.50997.5
5.31-156.80.04525081.53895

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.14data extraction
Cootmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→14.922 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2517 2367 10.01 %
Rwork0.2097 21277 -
obs0.2139 23644 96.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 148.8 Å2 / Biso mean: 43.031 Å2 / Biso min: 3.52 Å2
Refinement stepCycle: final / Resolution: 2.5→14.922 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3301 0 24 186 3511
Biso mean--54.41 28.95 -
Num. residues----430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023407
X-RAY DIFFRACTIONf_angle_d0.6194630
X-RAY DIFFRACTIONf_chiral_restr0.039515
X-RAY DIFFRACTIONf_plane_restr0.003584
X-RAY DIFFRACTIONf_dihedral_angle_d10.2661213
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.55020.35241320.28391215134796
2.5502-2.60540.27541370.26071233137096
2.6054-2.66560.32841380.24541216135496
2.6656-2.73190.26831350.25411196133195
2.7319-2.80530.29421340.26011202133694
2.8053-2.88730.32971300.24451204133494
2.8873-2.97980.30081370.24931213135094
2.9798-3.08540.27951350.26511209134495
3.0854-3.20770.25681400.24021271141197
3.2077-3.35220.25661390.22321252139198
3.3522-3.52670.25481440.20931283142799
3.5267-3.74440.2471420.20091276141899
3.7444-4.02820.26021420.1971282142498
4.0282-4.4240.21561450.16611282142798
4.424-5.04240.16721440.14671296144098
5.0424-6.27330.22831460.18551312145897
6.2733-14.92190.23141470.1881335148294
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)
13.1356-1.0968-0.60242.76220.22960.7922-0.04110.2807-0.0935-0.0943-0.0546-0.17430.03970.05820.10220.13690.00360.00040.17640.01050.1177-6.674763.7281110.289
22.24950.2917-1.16391.3268-0.2020.6603-0.82581.4548-0.6616-0.53960.4302-0.04250.5908-0.56960.26350.4788-0.30750.17420.9029-0.22630.4595-13.421931.6057105.6849
32.21930.409-0.99032.5994-1.01952.1006-0.0328-0.0004-0.1746-0.0376-0.07420.02330.0714-0.0530.09820.1190.00540.00840.18570.03350.1062-20.532759.8004127.5661
42.58330.4027-1.09952.05960.26062.1536-0.588-0.0814-1.6215-0.0146-0.0991-0.78070.47790.35890.48080.38370.04410.35440.422-0.02081.0409-12.686524.1575120.1499
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain H and resid 1:114H1 - 114
2X-RAY DIFFRACTION2chain H and resid 115:212H115 - 212
3X-RAY DIFFRACTION3chain L and resid 1:107L1 - 107
4X-RAY DIFFRACTION4chain L and resid 108:211L108 - 211

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