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- PDB-4pb9: Structure of the Fab fragment of the anti-Francisella tularensis ... -

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Basic information

Entry
Database: PDB / ID: 4pb9
TitleStructure of the Fab fragment of the anti-Francisella tularensis GroEL antibody Ab64
Components
  • Ab64 heavy chain
  • Ab64 light chain
KeywordsIMMUNE SYSTEM / antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 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 11, 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.d_res_high / _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: Ab64 heavy chain
L: Ab64 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2323
Polymers48,1362
Non-polymers961
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-44 kcal/mol
Surface area19800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.571, 154.571, 58.264
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Antibody Ab64 heavy chain


Mass: 23979.717 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
#2: Antibody Ab64 light chain


Mass: 24155.848 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
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.78 Å3/Da / Density % sol: 55.8 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Ab64 (27 mg/ml in 20 mM Tris pH 7.5, 0.15 M NaCl, and 0.02% NaN3) was mixed with reservoir (1.8 M ammonium sulfate and 0.1 M tris-HCl, pH 8.5) in hanging 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: Mar 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→15 Å / Num. obs: 15858 / % possible obs: 98.8 % / Redundancy: 5.8 % / Biso Wilson estimate: 48.91 Å2 / Rmerge(I) obs: 0.061 / Χ2: 1.316 / Net I/av σ(I): 28.977 / Net I/σ(I): 23 / Num. measured all: 91821
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.6-2.695.70.38615691.36197.5
2.69-2.85.70.29215551.4397.9
2.8-2.935.70.22315841.40798.6
2.93-3.085.80.16315991.35498.8
3.08-3.275.80.11415831.33899.1
3.27-3.525.80.0816031.2799.4
3.52-3.875.80.06115911.29999.8
3.87-4.425.90.04715931.23199
4.42-5.525.90.03715871.19599.3
5.52-155.80.02915941.28999

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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: 1.8.4_1496)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→14.848 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 0.07 / Phase error: 25.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2397 1562 10.01 %
Rwork0.1852 14046 -
obs0.1906 15608 97.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 159.22 Å2 / Biso mean: 61.9636 Å2 / Biso min: 22.27 Å2
Refinement stepCycle: final / Resolution: 2.6→14.848 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3326 0 5 34 3365
Biso mean--69.41 46.34 -
Num. residues----432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043417
X-RAY DIFFRACTIONf_angle_d0.7394645
X-RAY DIFFRACTIONf_chiral_restr0.028518
X-RAY DIFFRACTIONf_plane_restr0.003586
X-RAY DIFFRACTIONf_dihedral_angle_d10.6211212
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.67470.35511360.26891186132291
2.6747-2.76970.30911410.25111253139494
2.7697-2.87980.33451420.23231263140597
2.8798-3.00990.29291450.22481262140797
3.0099-3.16710.26011330.22941274140797
3.1671-3.36340.27221510.20781309146098
3.3634-3.61960.24641410.19461288142999
3.6196-3.97750.22921420.18171307144999
3.9775-4.53860.19421420.15641297143999
4.5386-5.66480.20941470.146213081455100
5.6648-14.84830.21271420.16421299144199
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)
11.6996-0.1756-1.32342.41860.38843.911-0.0190.06610.00730.0841-0.04980.34310.0084-0.6956-00.36710.0052-0.02190.4463-0.03210.4106-43.9257-38.42927.3039
21.3964-0.99190.14732.2621-0.05072.68180.1155-0.11040.5585-0.057-0.04140.3523-0.4907-0.06980.00030.66270.0377-0.00860.4943-0.11410.9367-43.5736-4.488523.5469
30.88590.08170.42324.21220.48142.1912-0.09940.26510.1035-0.58060.08830.0415-0.41210.0804-0.00130.51350.0083-0.00290.37510.04180.3358-29.0692-29.1431-5.325
42.14751.2711-1.49082.73650.19831.75660.1492-0.72030.22260.27130.0189-0.2781-0.42850.3821-0.00020.70540.0323-0.10660.5444-0.09830.6782-28.0815-7.350619.3546
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain L and resid 1:108L1 - 108
2X-RAY DIFFRACTION2chain L and resid 109:214L109 - 214
3X-RAY DIFFRACTION3chain H and resid 1:114H1 - 114
4X-RAY DIFFRACTION4chain H and resid 115:212H115 - 212

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