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- PDB-5vf6: Crystal structure of single chain variable fragment (scFv45). -

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Basic information

Entry
Database: PDB / ID: 5vf6
TitleCrystal structure of single chain variable fragment (scFv45).
Componentssingle chain variable fragment
KeywordsIMMUNE SYSTEM / single chain variable fragment / scFv / conformation-sensor antibodies / intrabodies
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.635 Å
AuthorsShrestha, O.K. / Tocilj, A. / Joshua-Tor, L. / Tonks, N.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM55989 United States
CitationJournal: Nat Commun / Year: 2018
Title: Harnessing insulin- and leptin-induced oxidation of PTP1B for therapeutic development.
Authors: Krishnan, N. / Bonham, C.A. / Rus, I.A. / Shrestha, O.K. / Gauss, C.M. / Haque, A. / Tocilj, A. / Joshua-Tor, L. / Tonks, N.K.
History
DepositionApr 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: single chain variable fragment


Theoretical massNumber of molelcules
Total (without water)25,5601
Polymers25,5601
Non-polymers00
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.232, 97.232, 61.260
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-573-

HOH

21A-620-

HOH

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Components

#1: Antibody single chain variable fragment / scFv45


Mass: 25559.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Escherichia coli K-12 (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 3.27 Å3/Da / Density % sol: 62.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 0.1M CAPS pH 10.0, 0.1M Ammonium Chloride, 40% PEG 400

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5419 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: May 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 1.635→42.103 Å / Num. obs: 37409 / % possible obs: 89.93 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 17.33
Reflection shellResolution: 1.64→1.69 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 2.56 / % possible all: 83.52

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P49

4p49


Resolution: 1.635→42.103 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.17
RfactorNum. reflection% reflection
Rfree0.1963 1803 4.82 %
Rwork0.1723 --
obs0.1735 37403 89.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.635→42.103 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1640 0 0 353 1993
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061673
X-RAY DIFFRACTIONf_angle_d0.812273
X-RAY DIFFRACTIONf_dihedral_angle_d9.947968
X-RAY DIFFRACTIONf_chiral_restr0.062248
X-RAY DIFFRACTIONf_plane_restr0.005300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6351-1.67930.26441130.2322530X-RAY DIFFRACTION83
1.6793-1.72880.25391220.22272573X-RAY DIFFRACTION85
1.7288-1.78460.23341500.20452617X-RAY DIFFRACTION88
1.7846-1.84830.22111450.18382711X-RAY DIFFRACTION90
1.8483-1.92240.21871230.18372779X-RAY DIFFRACTION92
1.9224-2.00980.19851780.1742813X-RAY DIFFRACTION94
2.0098-2.11580.1743840.16261477X-RAY DIFFRACTION49
2.1158-2.24840.20351560.15932940X-RAY DIFFRACTION98
2.2484-2.42190.19821340.17183024X-RAY DIFFRACTION99
2.4219-2.66560.18991360.17443043X-RAY DIFFRACTION99
2.6656-3.05130.21231450.16813050X-RAY DIFFRACTION100
3.0513-3.84380.1681510.16132881X-RAY DIFFRACTION93
3.8438-42.11660.17991660.16143162X-RAY DIFFRACTION100

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