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- PDB-6fp9: Crystal structure of anti-mTFP1 DARPin 1238_E11 -

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Basic information

Entry
Database: PDB / ID: 6fp9
TitleCrystal structure of anti-mTFP1 DARPin 1238_E11
ComponentsDARPin 1238_E11
KeywordsDE NOVO PROTEIN / Darpin / protein binder / designed ankyrin repeat proteins
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: 2.1 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

Downloads & links

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Assembly

Deposited unit
B: DARPin 1238_E11
A: DARPin 1238_E11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0416
Polymers39,7592
Non-polymers2824
Water7,782432
1
B: DARPin 1238_E11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9412
Polymers19,8791
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: DARPin 1238_E11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1004
Polymers19,8791
Non-polymers2203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.746, 91.597, 54.410
Angle α, β, γ (deg.)90.00, 116.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DARPin 1238_E11


Mass: 19879.373 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: DE NOVO PROTEIN, designed ankyrin repeat protein / Source: (gene. exp.) synthetic construct (others) / Plasmid: pQiq / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 432 / 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: 2.89 Å3/Da / Density % sol: 57.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.2 M (NH4)2SO4, 0.1 M MES pH 6.5, 20% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.1→48.51 Å / Num. obs: 25698 / % possible obs: 99.4 % / Redundancy: 3.7 % / CC1/2: 0.975 / Rrim(I) all: 0.273 / Net I/σ(I): 7.7
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1843 / Rrim(I) all: 1.54 / % possible all: 85.8

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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: 2.1→48.51 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.3
RfactorNum. reflection% reflection
Rfree0.2049 1308 5.09 %
Rwork0.1621 --
obs0.1643 25698 97.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→48.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2536 0 17 434 2987
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082612
X-RAY DIFFRACTIONf_angle_d0.8123544
X-RAY DIFFRACTIONf_dihedral_angle_d12.8621543
X-RAY DIFFRACTIONf_chiral_restr0.047407
X-RAY DIFFRACTIONf_plane_restr0.005463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.18410.28411220.24312427X-RAY DIFFRACTION87
2.1841-2.28350.25021380.21362645X-RAY DIFFRACTION95
2.2835-2.40390.23331460.18552713X-RAY DIFFRACTION98
2.4039-2.55450.21321600.16062733X-RAY DIFFRACTION99
2.5545-2.75170.1971560.1532739X-RAY DIFFRACTION99
2.7517-3.02860.2131510.15752755X-RAY DIFFRACTION99
3.0286-3.46670.20471630.14842763X-RAY DIFFRACTION99
3.4667-4.36720.14891250.12132794X-RAY DIFFRACTION99
4.3672-48.52320.18891470.16522821X-RAY DIFFRACTION99
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)
10.9650.0552-0.48391.0124-0.6651.07620.0417-0.1105-0.2281-0.04210.00010.05510.1217-0.06240.13070.0805-0.0221-0.01680.07060.04420.219960.3738-32.901120.1111
21.2484-0.10190.02321.65910.49981.59610.0288-0.1393-0.24620.0516-0.0182-0.03280.08260.00230.00320.0495-0.0126-0.01440.0320.01530.091858.7619-24.182819.0017
30.9005-0.2045-0.18731.32530.30110.80140.0231-0.11270.1649-0.0729-0.04380.066-0.0747-0.0072-0.00050.0631-0.01750.00720.0523-0.00210.067252.4077-8.044521.0541
44.17782.2447-0.45925.2523-0.82233.74120.07710.0010.44940.2119-0.01660.2248-0.1568-0.0418-0.04790.0717-0.021-0.01840.0741-0.06650.182951.91387.489127.7171
52.9665-1.32721.1141.007-0.0460.91410.059-0.1966-0.270.21770.00460.13440.029-0.1566-0.05780.0523-0.01160.00290.13440.02350.157688.1036-22.247321.1697
61.2567-0.08170.7230.819-0.00370.8035-0.08310.26860.0215-0.042-0.0189-0.0967-0.16320.22950.05890.0744-0.0237-0.01050.10790.04260.117183.3888-22.135713.3153
71.4275-0.76970.2540.991-0.23361.17020.03460.18250.0322-0.1584-0.1217-0.154-0.08780.16460.06560.11360.00490.00320.10950.01360.071974.6974-21.03563.6987
82.5122-0.15540.64732.2936-0.23172.14050.23790.2523-0.043-0.0573-0.03330.17120.0125-0.2602-0.13780.18540.04020.00910.20640.05960.090365.1431-17.3874-3.4419
90.71640.6877-0.84251.40130.19894.39-0.01340.05260.11840.11750.07620.2395-0.3769-0.4879-0.08930.17470.08580.030.23110.07710.108962.7647-10.3087-9.6598
102.5041-1.2537-0.28350.8233-0.00990.26460.0419-0.16380.06280.0174-0.0708-0.0660.04320.0046-0.13670.1464-0.07570.0840.29620.06320.311471.3856-23.3063-18.643
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 14 through 37 )
2X-RAY DIFFRACTION2chain 'B' and (resid 38 through 70 )
3X-RAY DIFFRACTION3chain 'B' and (resid 71 through 160 )
4X-RAY DIFFRACTION4chain 'B' and (resid 161 through 176 )
5X-RAY DIFFRACTION5chain 'A' and (resid 12 through 37 )
6X-RAY DIFFRACTION6chain 'A' and (resid 38 through 70 )
7X-RAY DIFFRACTION7chain 'A' and (resid 71 through 127 )
8X-RAY DIFFRACTION8chain 'A' and (resid 128 through 160 )
9X-RAY DIFFRACTION9chain 'A' and (resid 161 through 173 )
10X-RAY DIFFRACTION10chain 'A' and (resid 174 through 182 )

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