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- PDB-5le4: Crystal structure of DARPin-DARPin rigid fusion, variant DD_D12_11_D12 -

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Basic information

Entry
Database: PDB / ID: 5le4
TitleCrystal structure of DARPin-DARPin rigid fusion, variant DD_D12_11_D12
ComponentsDD_D12_11_D12
KeywordsDE NOVO PROTEIN / X-ray crystallography / designed ankyrin repeat proteins / protein design / protein engineering / rigid domain fusions
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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: DD_D12_11_D12


Theoretical massNumber of molelcules
Total (without water)35,1611
Polymers35,1611
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.290, 57.080, 147.560
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_11_D12


Mass: 35160.637 Da / Num. of mol.: 1
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: 3.25 Å3/Da / Density % sol: 62.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 3350 18% w/v, KSCN 0.15 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: Oct 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→43.727 Å / Num. obs: 19812 / % possible obs: 99.68 % / Redundancy: 12.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.104 / Net I/σ(I): 14.16
Reflection shellResolution: 2.35→2.434 Å / Rmerge(I) obs: 5.309

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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: 2.35→43.727 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 41.04
RfactorNum. reflection% reflection
Rfree0.2717 991 5.02 %
Rwork0.2324 --
obs0.2342 19756 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.35→43.727 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2375 0 0 0 2375
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022416
X-RAY DIFFRACTIONf_angle_d0.4643282
X-RAY DIFFRACTIONf_dihedral_angle_d12.431427
X-RAY DIFFRACTIONf_chiral_restr0.033382
X-RAY DIFFRACTIONf_plane_restr0.002432
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.47390.61171400.51182629X-RAY DIFFRACTION99
2.4739-2.62890.4671380.41572620X-RAY DIFFRACTION100
2.6289-2.83180.39421400.36192644X-RAY DIFFRACTION100
2.8318-3.11670.34851390.2842636X-RAY DIFFRACTION100
3.1167-3.56750.25041410.25642692X-RAY DIFFRACTION100
3.5675-4.4940.21791430.20942699X-RAY DIFFRACTION100
4.494-43.7350.24431500.18132845X-RAY DIFFRACTION100
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)
12.60650.2118-0.7592.9137-0.33244.45790.05240.2324-0.2773-0.9404-0.0842-0.0090.0962-0.23810.04681.04090.0029-0.02470.7066-0.05920.67190.939862.8639162.8629
24.1239-1.872.36322.495-1.50054.7209-0.3907-0.34770.37510.52250.16810.2471-0.2819-0.25010.12880.9907-0.12010.01090.83440.13630.793-2.601255.0006190.2163
33.20661.28830.66712.90260.68921.0860.29370.03780.21610.825-0.3897-0.38890.11140.23320.06770.936-0.1258-0.12240.88080.09990.778913.998158.2769198.7644
41.35020.58110.25551.0890.00271.0209-0.38650.15971.30550.6761-0.1149-0.9204-0.28340.27740.33681.4968-0.3577-0.51021.2140.18121.73126.114275.9256204.8342
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 158 )
2X-RAY DIFFRACTION2chain 'A' and (resid 159 through 181 )
3X-RAY DIFFRACTION3chain 'A' and (resid 182 through 259 )
4X-RAY DIFFRACTION4chain 'A' and (resid 260 through 325 )

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