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- PDB-4p49: The structure of a chicken anti-prostate specific antigen scFv -

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Basic information

Entry
Database: PDB / ID: 4p49
TitleThe structure of a chicken anti-prostate specific antigen scFv
ComponentsAntibody scFv B8
KeywordsIMMUNE SYSTEM / recombinant antibody / chicken / cardiac troponin I / scFv / immunoglobulin / phage display
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION
Function and homology information
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsConroy, P.J. / Law, R.H.P. / Gilgunn, S. / Hearty, S. / Llyod, G. / Caradoc-Davies, T.T. / O'Kennedy, R.J. / Whisstock, J.C.
Funding support Ireland, 1items
OrganizationGrant numberCountry
SFI10/CE/B1821 Ireland
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 1.2Aug 6, 2014Group: Structure summary
Revision 1.3Oct 1, 2014Group: Database references
Revision 1.4Jan 14, 2015Group: Database references
Revision 1.5Feb 4, 2015Group: Derived calculations
Revision 1.6Sep 27, 2017Group: Advisory / Data collection ...Advisory / 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 / pdbx_validate_symm_contact / 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 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2 / _software.classification
Revision 1.7Dec 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

Downloads & links

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Assembly

Deposited unit
A: Antibody scFv B8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0126
Polymers27,5691
Non-polymers4435
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.459, 52.459, 302.375
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
11A-406-

HOH

21A-409-

HOH

31A-478-

HOH

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Components

#1: Antibody Antibody scFv B8


Mass: 27568.896 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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 43.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 0.1M NaOAc pH 4.6, 0.2M NH4-sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953697 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953697 Å / Relative weight: 1
ReflectionResolution: 1.4→50.396 Å / Num. all: 50126 / Num. obs: 50126 / % possible obs: 99.5 % / Redundancy: 17.7 % / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.029 / Rrim(I) all: 0.129 / Rsym value: 0.126 / Net I/av σ(I): 3.273 / Net I/σ(I): 12.9 / Num. measured all: 887042
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.4-1.489.10.910.96214068540.3130.912.396.3
1.48-1.57140.6031.39525467810.1650.6034.1100
1.57-1.6720.40.393213031264030.0890.3937.1100
1.67-1.8120.50.249312337760110.0560.24910.2100
1.81-1.9820.40.172411340255470.0390.17214.6100
1.98-2.2120.30.1424.610306450700.0320.14218.9100
2.21-2.5620.10.12859067945130.0290.12821.1100
2.56-3.1319.70.1274.97682239070.0290.12723.8100
3.13-4.4318.80.0986.15835631110.0230.09826.4100
4.43-151.18817.40.0796.63363619290.0190.07924.7100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALA3.3.21data scaling
Blu-Icedata collection
XDSdata scaling
PDB_EXTRACT3.14data extraction
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→50.396 Å / FOM work R set: 0.8762 / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2138 2507 5.02 %
Rwork0.1829 47434 -
obs0.1845 49941 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.76 Å2 / Biso mean: 22.98 Å2 / Biso min: 7.94 Å2
Refinement stepCycle: final / Resolution: 1.4→50.396 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1639 0 24 331 1994
Biso mean--45.36 35.67 -
Num. residues----226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061741
X-RAY DIFFRACTIONf_angle_d1.0212372
X-RAY DIFFRACTIONf_chiral_restr0.039260
X-RAY DIFFRACTIONf_plane_restr0.004309
X-RAY DIFFRACTIONf_dihedral_angle_d12.271597
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.42690.32341480.30772354250292
1.4269-1.45610.33691210.26122522264397
1.4561-1.48770.2921360.24882542267899
1.4877-1.52230.24621270.230525952722100
1.5223-1.56040.23791340.208225982732100
1.5604-1.60260.20381290.200626022731100
1.6026-1.64980.23531140.198426452759100
1.6498-1.7030.2341560.198225622718100
1.703-1.76390.24621480.191726152763100
1.7639-1.83450.21541380.19326032741100
1.8345-1.9180.22831330.193126442777100
1.918-2.01910.21681350.184726772812100
2.0191-2.14560.21171350.183926132748100
2.1456-2.31130.22981440.184526802824100
2.3113-2.54390.23061500.18726732823100
2.5439-2.9120.19111360.1827462882100
2.912-3.66860.18641480.159327602908100
3.6686-50.42850.19171750.159830033178100
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)
11.6657-0.1142-0.23661.5063-0.20760.9733-0.0563-0.0519-0.03050.02550.0326-0.07920.01910.06820.02890.07140.0045-0.00110.0751-0.02120.08995.518929.02894.8962
22.0215-0.4-0.67161.1579-0.43991.3594-0.0759-0.1855-0.1049-0.04080.05130.01230.05220.04160.02640.09260.00790.00070.0907-0.02260.08973.416226.70235.616
30.3256-0.09240.12821.475-0.25491.3537-0.0413-0.3366-0.3550.36860.06390.0894-0.1345-0.2074-0.04260.26740.07640.05450.22640.06070.1906-9.413433.013622.889
40.5957-0.3127-0.12321.5114-0.80281.2424-0.1446-0.12910.08450.52150.37470.2986-0.4484-0.33190.2790.23490.10830.04640.18010.0130.1227-11.502641.153714.2521
51.423-0.3906-0.10011.4259-0.62560.8818-0.07650.16030.04830.07140.45840.5659-0.1778-0.52520.01330.15140.04330.01490.23310.06520.1749-13.795731.702316.7432
61.27160.1553-0.7711.5689-1.3092.4419-0.0126-0.09410.00410.19890.17220.0754-0.1101-0.1983-0.08130.16040.0250.00330.1523-0.01050.1307-5.826236.751613.3489
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 64 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 65 through 101 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 102 through 137 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 138 through 204 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 205 through 220 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 221 through 243 )A0

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