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- PDB-6fpb: Crystal structure of anti-mTFP1 DARPin 1238_G01 in space group I4 -

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Basic information

Entry
Database: PDB / ID: 6fpb
TitleCrystal structure of anti-mTFP1 DARPin 1238_G01 in space group I4
ComponentsDARPin 1238_G01
KeywordsDE NOVO PROTEIN / Darpin / protein binder / designed ankyrin repeat protein
Function / homologyAnkyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.617 Å
AuthorsJakob, R.P. / Vigano, M.A. / Bieli, D. / Matsuda, S. / Schaefer, J.V. / Pluckthun, A. / Affolter, M. / Maier, T.
CitationJournal: Biol Open / Year: 2018
Title: DARPins recognizing mTFP1 as novel reagents forin vitroandin vivoprotein manipulations.
Authors: Vigano, M.A. / Bieli, D. / Schaefer, J.V. / Jakob, R.P. / Matsuda, S. / Maier, T. / Pluckthun, A. / Affolter, M.
History
DepositionFeb 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 26, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.3Jan 17, 2024Group: 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: DARPin 1238_G01
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4002
Polymers17,3651
Non-polymers351
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-10 kcal/mol
Surface area7910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.224, 66.224, 77.913
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein DARPin 1238_G01


Mass: 17364.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pQiq / Production host: Escherichia coli (E. coli) / Strain (production host): XL1Blue
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.46 Å3/Da / Density % sol: 49.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 2 M NaCl, 10% PEG10000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99986 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99986 Å / Relative weight: 1
ReflectionResolution: 1.617→46.827 Å / Num. obs: 41912 / % possible obs: 99.3 % / Redundancy: 2.2 % / CC1/2: 0.998 / Rrim(I) all: 0.066 / Net I/σ(I): 11.5
Reflection shellResolution: 1.617→1.72 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4096 / CC1/2: 0.746 / Rrim(I) all: 0.935 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX(1.10pre_2131: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YDY

4ydy


Resolution: 1.617→46.827 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.97
RfactorNum. reflection% reflection
Rfree0.1746 2097 5 %
Rwork0.1514 --
obs0.1526 41912 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.617→46.827 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1197 0 1 196 1394
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091221
X-RAY DIFFRACTIONf_angle_d1.0171658
X-RAY DIFFRACTIONf_dihedral_angle_d10.235733
X-RAY DIFFRACTIONf_chiral_restr0.055194
X-RAY DIFFRACTIONf_plane_restr0.007220
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6175-1.65510.34541290.33652498X-RAY DIFFRACTION92
1.6551-1.69650.32141420.30422668X-RAY DIFFRACTION100
1.6965-1.74240.3731410.26062682X-RAY DIFFRACTION100
1.7424-1.79360.24421370.24582657X-RAY DIFFRACTION100
1.7936-1.85150.25551410.21322656X-RAY DIFFRACTION100
1.8515-1.91770.29061410.20582652X-RAY DIFFRACTION100
1.9177-1.99450.19551410.18242711X-RAY DIFFRACTION100
1.9945-2.08530.19281360.16682639X-RAY DIFFRACTION100
2.0853-2.19520.21751440.16042691X-RAY DIFFRACTION100
2.1952-2.33270.18051440.15762685X-RAY DIFFRACTION100
2.3327-2.51280.17081430.14742672X-RAY DIFFRACTION100
2.5128-2.76570.1671390.1442652X-RAY DIFFRACTION99
2.7657-3.16580.14421420.14652648X-RAY DIFFRACTION100
3.1658-3.98830.1521340.12472646X-RAY DIFFRACTION99
3.9883-46.84710.15871430.13642658X-RAY DIFFRACTION98
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)
13.89842.6189-0.50081.9542-0.40250.12010.00720.07740.2298-0.0250.07610.065-0.505-0.1248-0.19210.3948-0.0972-0.00440.37160.03880.32414.476421.161417.3917
27.94035.0903-3.92926.5747-3.73076.5976-0.19570.11410.2107-0.84090.25240.44440.4104-0.3858-0.09840.3604-0.05570.00960.34870.04320.298814.120616.11029.0542
30.37590.1916-0.40522.9045-1.79631.970.0053-0.01840.0477-0.1309-0.1694-0.259-0.03280.48270.13760.2053-0.0579-0.00280.36680.02380.289819.79466.419225.3596
41.1035-0.0393-0.15421.697-0.12390.7750.099-0.2785-0.02920.4528-0.3144-0.25240.24450.60770.06980.30680.0095-0.06570.44160.08960.313219.2565-6.301940.6573
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 14 )
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 25 )
3X-RAY DIFFRACTION3chain 'A' and (resid 26 through 125 )
4X-RAY DIFFRACTION4chain 'A' and (resid 126 through 161 )

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