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

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Basic information

Entry
Database: PDB / ID: 5leb
TitleCrystal structure of DARPin-DARPin rigid fusion, variant DDD_D12_06_D12_06_D12
ComponentsDDD_D12_06_D12_06_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: 2.3 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_06_D12_06_D12


Theoretical massNumber of molelcules
Total (without water)50,5231
Polymers50,5231
Non-polymers00
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area21170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.120, 29.470, 146.870
Angle α, β, γ (deg.)90.00, 107.47, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein DDD_D12_06_D12_06_D12


Mass: 50522.777 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
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.64 Å3/Da / Density % sol: 53.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 8000 10.0% w/v, PEG 1000 10.0% w/v, Sodium acetate 0.3 M, Sodium cacodylate 0.1 M, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→35.343 Å / Num. obs: 24249 / % possible obs: 99.79 % / Redundancy: 6.6 % / CC1/2: 1 / Rmerge(I) obs: 0.073 / Net I/σ(I): 18.17
Reflection shellResolution: 2.3→2.382 Å / Rmerge(I) obs: 1.931

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX(dev_2398)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SVX chain A

1svx


Resolution: 2.3→35.343 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.6
RfactorNum. reflection% reflection
Rfree0.2412 1213 5.01 %
Rwork0.2113 --
obs0.2127 24222 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→35.343 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3469 0 0 26 3495
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023531
X-RAY DIFFRACTIONf_angle_d0.4254808
X-RAY DIFFRACTIONf_dihedral_angle_d10.8682071
X-RAY DIFFRACTIONf_chiral_restr0.033560
X-RAY DIFFRACTIONf_plane_restr0.002636
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.39210.42351320.40132495X-RAY DIFFRACTION100
2.3921-2.50090.36921330.32192518X-RAY DIFFRACTION100
2.5009-2.63270.31561340.29582536X-RAY DIFFRACTION100
2.6327-2.79760.30331310.28782506X-RAY DIFFRACTION100
2.7976-3.01350.32551360.28342572X-RAY DIFFRACTION100
3.0135-3.31660.27171330.26752537X-RAY DIFFRACTION100
3.3166-3.7960.24541350.21782552X-RAY DIFFRACTION100
3.796-4.78070.18371360.15742595X-RAY DIFFRACTION100
4.7807-35.34730.1971430.16132698X-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)
11.49880.35050.1652.79251.75956.88550.1983-0.0817-0.01130.1586-0.147-0.31410.44290.3484-0.03450.37840.00120.00030.33250.1030.4752-64.0461-45.6432139.6224
28.42512.63256.0822.43011.30815.41990.5382-0.87990.06320.3165-0.430.14570.4227-0.5777-0.0670.6552-0.1640.00890.5540.01240.4098-46.9666-33.943171.936
31.7249-0.1586-0.14181.97182.38969.26760.0678-0.1784-0.04640.24190.3585-0.28070.65890.9956-0.42410.4430.033-0.02640.5678-0.0360.552-22.5312-24.95202.7437
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 176 )
2X-RAY DIFFRACTION2chain 'A' and (resid 177 through 286 )
3X-RAY DIFFRACTION3chain 'A' and (resid 287 through 473 )

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