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- PDB-4p48: The structure of a chicken anti-cardiac Troponin I scFv -

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Basic information

Entry
Database: PDB / ID: 4p48
TitleThe structure of a chicken anti-cardiac Troponin I scFv
ComponentsAntibody scFv 180
KeywordsIMMUNE SYSTEM / recombinant antibody chicken / cardiac troponin I / scFv / immunoglobulin / phage display
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 Å
AuthorsConroy, P.J. / Law, R.H.P. / Gillgunn, S. / Hearty, S. / Caradoc-Davies, T.T. / Llyod, G. / O'Kennedy, R.J. / Whisstock, J.C.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Reconciling the structural attributes of avian antibodies.
Authors: Conroy, P.J. / Law, R.H. / Gilgunn, S. / Hearty, S. / Caradoc-Davies, T.T. / Lloyd, G. / O'Kennedy, R.J. / Whisstock, J.C.
History
DepositionMar 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
Revision 1.2Oct 1, 2014Group: Database references
Revision 1.3Jan 14, 2015Group: Database references
Revision 1.4Feb 4, 2015Group: Derived calculations
Revision 1.5Sep 27, 2017Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.6Dec 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.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antibody scFv 180


Theoretical massNumber of molelcules
Total (without water)28,4951
Polymers28,4951
Non-polymers00
Water6,503361
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.780, 58.379, 69.048
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 Antibody scFv 180


Mass: 28494.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: pComb3x / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 361 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.83 Å3/Da / Density % sol: 32.83 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 9.6
Details: 0.1M Tris-HCl pH9.6, 0.2M NaOAc, 29% (w/v) PEG 4000 with 0.1M glycine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953689 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 12, 2012
RadiationMonochromator: Double crystal monochromator (Si111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953689 Å / Relative weight: 1
ReflectionResolution: 1.35→19.9 Å / Num. obs: 46638 / % possible obs: 99.97 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 14.57
Reflection shellResolution: 1.35→1.42 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 4.2 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
Blu-Ice2.5.1data collection
XDSdata scaling
PDB_EXTRACT3.14data extraction
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→19.787 Å / FOM work R set: 0.9077 / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1759 2360 5.06 %
Rwork0.156 44278 -
obs0.157 46638 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 48.25 Å2 / Biso mean: 10.26 Å2 / Biso min: 1.12 Å2
Refinement stepCycle: final / Resolution: 1.35→19.787 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1719 0 361 0 2080
Biso mean--21.81 --
Num. residues----235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011831
X-RAY DIFFRACTIONf_angle_d1.272500
X-RAY DIFFRACTIONf_chiral_restr0.085270
X-RAY DIFFRACTIONf_plane_restr0.007334
X-RAY DIFFRACTIONf_dihedral_angle_d11.606644
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.35-1.37760.23641380.213525422680
1.3776-1.40750.2251200.181925822702
1.4075-1.44020.22151300.179226052735
1.4402-1.47620.17421300.172625422672
1.4762-1.51610.19721400.166925822722
1.5161-1.56070.17311400.156826052745
1.5607-1.61110.18881400.153325462686
1.6111-1.66870.19131430.149925972740
1.6687-1.73540.15621360.151725782714
1.7354-1.81440.17861500.155425732723
1.8144-1.90990.17071390.155425962735
1.9099-2.02950.17211340.148826072741
2.0295-2.1860.19581440.149425942738
2.186-2.40570.17361470.159426192766
2.4057-2.7530.16171430.160426402783
2.753-3.46540.17141290.157426952824
3.4654-19.78910.15981570.141927752932
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)
10.5253-0.0395-0.07930.43560.1870.0877-0.00730.0264-0.0538-0.0338-0.017-0.01830.02420.0608-0.00090.02510.00320.0120.04150.00950.029238.72-10.0283-2.2047
20.3674-0.1187-0.1520.38620.0710.33010.0171-0.00390.0410.0132-0.01240.005-0.04970.003-0.00390.02640.00090.0080.02830.00750.028334.91171.96915.9153
30.3932-0.0177-0.03081.2074-0.61131.04660.01940.0340.0141-0.01730.05530.2055-0.0103-0.18-0.03380.05450.00130.02760.0596-0.00360.087420.38387.814513.1777
40.63190.1074-0.16680.4278-0.1890.52130.0486-0.01610.0286-0.0306-0.03620.0026-0.06490.05890.0170.03710.00350.01370.02480.00530.030433.58085.9758.0865
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 33 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 204 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 205 through 219 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 220 through 250 )A0

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