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- PDB-5le9: Crystal structure of DARPin-DARPin rigid fusion, variant DD_Off7_... -

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Basic information

Entry
Database: PDB / ID: 5le9
TitleCrystal structure of DARPin-DARPin rigid fusion, variant DD_Off7_09_3G124
ComponentsDD_Off7_09_3G124
KeywordsDE NOVO PROTEIN / designed ankyrin repeat proteins / protein design / protein engineering / rigid domain fusions
Function / homologyACETATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsBatyuk, A. / Wu, Y. / Mittl, P.R. / Plueckthun, A.
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_Off7_09_3G124
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3948
Polymers34,9801
Non-polymers4137
Water2,234124
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.980, 71.980, 128.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein DD_Off7_09_3G124


Mass: 34980.469 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.37 Å3/Da / Density % sol: 48.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: MPD 30% v/v, Sodium chloride 0.2 M, Sodium acetate trihydrate 0.1 M, pH 4.6

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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: Dec 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→39.859 Å / Num. obs: 29498 / % possible obs: 99.44 % / Redundancy: 24.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1782 / Net I/σ(I): 13.26
Reflection shellResolution: 1.85→1.916 Å / Rmerge(I) obs: 18.36

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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: 1.85→39.859 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.16
RfactorNum. reflection% reflection
Rfree0.245 1471 5.01 %
Rwork0.2257 --
obs0.2267 29365 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→39.859 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2396 0 28 124 2548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022480
X-RAY DIFFRACTIONf_angle_d0.4263370
X-RAY DIFFRACTIONf_dihedral_angle_d9.5941449
X-RAY DIFFRACTIONf_chiral_restr0.034384
X-RAY DIFFRACTIONf_plane_restr0.003447
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8501-1.90980.54941300.60682436X-RAY DIFFRACTION98
1.9098-1.9780.40751280.41752451X-RAY DIFFRACTION99
1.978-2.05720.34491320.34112500X-RAY DIFFRACTION99
2.0572-2.15090.28311300.30842476X-RAY DIFFRACTION100
2.1509-2.26430.29871340.28922525X-RAY DIFFRACTION100
2.2643-2.40610.36791320.26572519X-RAY DIFFRACTION100
2.4061-2.59180.27041330.24062512X-RAY DIFFRACTION100
2.5918-2.85260.27181340.22542541X-RAY DIFFRACTION100
2.8526-3.26520.26511360.22342586X-RAY DIFFRACTION100
3.2652-4.11320.22021360.18312587X-RAY DIFFRACTION100
4.1132-39.86810.19131460.19512761X-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)
10.9935-0.8801-0.76981.34840.70541.00990.02580.09650.0113-0.2060.0763-0.124-0.15050.0434-00.4293-0.01510.04740.48130.01120.446814.62470.751910.1563
20.924-0.96570.02162.65791.57981.5443-0.3717-0.21660.13680.82980.3778-0.06670.63860.2434-0.02060.55310.142-0.00390.4018-0.00790.375.204717.056950.4879
30.98790.0395-0.78010.13510.14391.064-0.6001-0.6315-0.1820.30980.3096-0.21990.99120.4706-0.73111.49140.7157-0.03171.1376-0.08490.28084.518424.325874.5709
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 158 )
2X-RAY DIFFRACTION2chain 'A' and (resid 159 through 303 )
3X-RAY DIFFRACTION3chain 'A' and (resid 304 through 322 )

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