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- PDB-5le3: Crystal structure of DARPin-DARPin rigid fusion, variant DD_D12_09_D12 -

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Basic information

Entry
Database: PDB / ID: 5le3
TitleCrystal structure of DARPin-DARPin rigid fusion, variant DD_D12_09_D12
ComponentsDD_D12_09_D12
KeywordsDE NOVO PROTEIN / designed ankyrin repeat proteins / protein design / protein engineering / rigid domain fusions
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 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 1.2Sep 18, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.pdbx_CC_half
Revision 1.3Jan 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: DD_D12_09_D12
B: DD_D12_09_D12
C: DD_D12_09_D12
D: DD_D12_09_D12


Theoretical massNumber of molelcules
Total (without water)134,3634
Polymers134,3634
Non-polymers00
Water00
1
A: DD_D12_09_D12


Theoretical massNumber of molelcules
Total (without water)33,5911
Polymers33,5911
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DD_D12_09_D12


Theoretical massNumber of molelcules
Total (without water)33,5911
Polymers33,5911
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: DD_D12_09_D12


Theoretical massNumber of molelcules
Total (without water)33,5911
Polymers33,5911
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: DD_D12_09_D12


Theoretical massNumber of molelcules
Total (without water)33,5911
Polymers33,5911
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.220, 108.790, 129.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
DD_D12_09_D12


Mass: 33590.656 Da / Num. of mol.: 4
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

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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: 2.54 Å3/Da / Density % sol: 51.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: PEG 3350 15.9% w/v, Sodium fluoride 0.2 M, Bis-Tris propane 0.1 M, pH 6.3

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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: Jun 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→48.61 Å / Num. obs: 17776 / % possible obs: 98.51 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.2413 / Net I/σ(I): 7.96
Reflection shellResolution: 3.5→3.625 Å / Rmerge(I) obs: 12.98 / CC1/2: 0.387

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Processing

Software
NameVersionClassification
PHENIX(dev_2456: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SVX chain A

1svx


Resolution: 3.5→48.61 Å / SU ML: 0.77 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 50.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3488 878 5 %
Rwork0.3033 --
obs0.3056 17573 98.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5→48.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9100 0 0 0 9100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029260
X-RAY DIFFRACTIONf_angle_d0.63812608
X-RAY DIFFRACTIONf_dihedral_angle_d8.1635420
X-RAY DIFFRACTIONf_chiral_restr0.0381472
X-RAY DIFFRACTIONf_plane_restr0.0041668
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.71920.53111420.50952707X-RAY DIFFRACTION98
3.7192-4.00630.50021400.43982689X-RAY DIFFRACTION97
4.0063-4.40920.39341460.37412751X-RAY DIFFRACTION99
4.4092-5.04670.44091440.33762775X-RAY DIFFRACTION99
5.0467-6.3560.42511500.39142823X-RAY DIFFRACTION99
6.356-48.61470.26551560.22412950X-RAY DIFFRACTION99

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