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- PDB-5lea: Crystal structure of DARPin-DARPin rigid fusion, variant DD_Off7_... -

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Basic information

Entry
Database: PDB / ID: 5lea
TitleCrystal structure of DARPin-DARPin rigid fusion, variant DD_Off7_12_3G124
ComponentsDD_Off7_12_3G124
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: 2.4 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

Downloads & links

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Assembly

Deposited unit
A: DD_Off7_12_3G124
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5023
Polymers35,2661
Non-polymers2362
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint-12 kcal/mol
Surface area15290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.410, 46.400, 63.080
Angle α, β, γ (deg.)90.00, 111.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DD_Off7_12_3G124


Mass: 35265.805 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: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.42 Å3/Da / Density % sol: 49.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: MPD 32.3% v/v, Sodium Chloride 0.2 M, Sodium acetate trihydrate 0.1 M, pH 5.0

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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: Mar 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→36.437 Å / Num. obs: 13295 / % possible obs: 99 % / Redundancy: 4.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.094 / Net I/σ(I): 9.4
Reflection shellResolution: 2.4→2.486 Å / Rmerge(I) obs: 1.381

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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: 2.4→36.437 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.71
RfactorNum. reflection% reflection
Rfree0.2843 665 5.01 %
Rwork0.236 --
obs0.2386 13281 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→36.437 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2391 0 16 17 2424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022447
X-RAY DIFFRACTIONf_angle_d0.463326
X-RAY DIFFRACTIONf_dihedral_angle_d10.1731448
X-RAY DIFFRACTIONf_chiral_restr0.034384
X-RAY DIFFRACTIONf_plane_restr0.003434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.58530.38021320.32072511X-RAY DIFFRACTION99
2.5853-2.84540.36351320.2962503X-RAY DIFFRACTION100
2.8454-3.25690.3731340.27592531X-RAY DIFFRACTION100
3.2569-4.10250.22791310.23222496X-RAY DIFFRACTION98
4.1025-36.44130.26451360.20372575X-RAY DIFFRACTION98
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)
11.6991-0.82380.49746.7604-3.8774.3185-0.0160.03130.07170.14090.28220.2675-0.1729-0.1199-0.22330.35810.0173-0.00560.3478-0.01290.34658.696-14.918520.3447
25.1474-0.3146-1.56881.58911.95853.1679-0.2308-1.0056-0.7797-0.03950.05030.4127-0.3784-0.8190.14070.64230.2473-0.03981.06510.08030.7485-21.269817.458910.1734
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 182 )
2X-RAY DIFFRACTION2chain 'A' and (resid 183 through 327 )

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