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- PDB-5le2: Crystal structure of DARPin-DARPin rigid fusion, variant DDD_D12_... -

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Basic information

Entry
Database: PDB / ID: 5le2
TitleCrystal structure of DARPin-DARPin rigid fusion, variant DDD_D12_15_D12_15_D12
ComponentsDDD_D12_15_D12_15_D12
KeywordsDE NOVO PROTEIN / X-ray crystallography / designed ankyrin repeat proteins / protein design / protein engineering / rigid domain fusions
Function / homologyAnkyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha / ACETATE ION / THIOCYANATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBatyuk, A. / Wu, Y. / Mittl, P.R. / Plueckthun, A.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B_166676 Switzerland
European Research CouncilNEXTBINDERS
CitationJournal: Sci Rep / Year: 2017
Title: Rigidly connected multispecific artificial binders with adjustable geometries.
Authors: Wu, Y. / Batyuk, A. / Honegger, A. / Brandl, F. / Mittl, P.R.E. / Pluckthun, A.
History
DepositionJun 29, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 10, 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: DDD_D12_15_D12_15_D12
B: DDD_D12_15_D12_15_D12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,4995
Polymers106,3232
Non-polymers1753
Water91951
1
A: DDD_D12_15_D12_15_D12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3374
Polymers53,1621
Non-polymers1753
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DDD_D12_15_D12_15_D12


Theoretical massNumber of molelcules
Total (without water)53,1621
Polymers53,1621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.970, 53.790, 144.000
Angle α, β, γ (deg.)90.00, 107.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DDD_D12_15_D12_15_D12


Mass: 53161.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): XL1-Blue
#2: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#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.: 51 / 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: 3.24 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 8000 10.0%, PEG 1000 10.0%, KSCN 0.2 M, Tris (HOAc) 0.1 M, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→47.999 Å / Num. obs: 53205 / % possible obs: 97.8 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.1987 / Net I/σ(I): 6.13
Reflection shellResolution: 2.4→2.486 Å / Rmerge(I) obs: 12.4

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX(dev_2386)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SVX chain A

1svx


Resolution: 2.4→47.999 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 40.7
RfactorNum. reflection% reflection
Rfree0.2809 2632 4.99 %
Rwork0.2476 --
obs0.2493 52693 97.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→47.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7294 0 10 51 7355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037421
X-RAY DIFFRACTIONf_angle_d0.46510073
X-RAY DIFFRACTIONf_dihedral_angle_d9.9264410
X-RAY DIFFRACTIONf_chiral_restr0.0341162
X-RAY DIFFRACTIONf_plane_restr0.0021335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.44370.56821220.53432376X-RAY DIFFRACTION87
2.4437-2.49070.45751300.49542444X-RAY DIFFRACTION94
2.4907-2.54150.45841370.44682596X-RAY DIFFRACTION97
2.5415-2.59680.4241370.40482579X-RAY DIFFRACTION97
2.5968-2.65720.42631380.37662630X-RAY DIFFRACTION99
2.6572-2.72370.39681360.37462613X-RAY DIFFRACTION97
2.7237-2.79730.37461390.38472649X-RAY DIFFRACTION99
2.7973-2.87960.39831370.37642600X-RAY DIFFRACTION98
2.8796-2.97250.40041410.38352670X-RAY DIFFRACTION99
2.9725-3.07870.34651400.34412654X-RAY DIFFRACTION99
3.0787-3.2020.41631390.33952648X-RAY DIFFRACTION99
3.202-3.34770.35021420.30892690X-RAY DIFFRACTION100
3.3477-3.52410.30851390.28482640X-RAY DIFFRACTION99
3.5241-3.74480.31811390.25082662X-RAY DIFFRACTION99
3.7448-4.03390.23751410.21452698X-RAY DIFFRACTION99
4.0339-4.43950.2221420.18882702X-RAY DIFFRACTION99
4.4395-5.08130.21831410.1772686X-RAY DIFFRACTION99
5.0813-6.39950.23711440.2162724X-RAY DIFFRACTION99
6.3995-48.00820.20131480.16752800X-RAY DIFFRACTION98

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