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- PDB-5le8: Crystal structure of DARPin-DARPin rigid fusion, variant DD_D12_15_D12 -

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Basic information

Entry
Database: PDB / ID: 5le8
TitleCrystal structure of DARPin-DARPin rigid fusion, variant DD_D12_15_D12
ComponentsDD_D12_15_D12
KeywordsDE NOVO PROTEIN / designed ankyrin repeat proteins / protein design / protein engineering / rigid domain fusions
Function / homologyAnkyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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_15_D12
B: DD_D12_15_D12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,08321
Polymers71,2142
Non-polymers1,86919
Water9,584532
1
A: DD_D12_15_D12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,46810
Polymers35,6071
Non-polymers8619
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DD_D12_15_D12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,61611
Polymers35,6071
Non-polymers1,00910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.760, 73.540, 77.980
Angle α, β, γ (deg.)96.03, 103.43, 89.52
Int Tables number1
Space group name H-MP1

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Components

#1: Protein DD_D12_15_D12


Mass: 35606.969 Da / Num. of mol.: 2
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 532 / 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: 4.26 Å3/Da / Density % sol: 71.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 3350 20% w/v, Sodium citrate 0.2 M, Bis-Tris propane 0.1 M, pH 8.5

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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: 1.78→43.39 Å / Num. obs: 109030 / % possible obs: 95.44 % / Redundancy: 3.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.081 / Net I/σ(I): 8.62
Reflection shellResolution: 1.78→1.844 Å / Rmerge(I) obs: 2.774

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX(dev_2405:)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SVX chain A

1svx


Resolution: 1.78→43.39 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 29.96
RfactorNum. reflection% reflection
Rfree0.2052 5382 5 %
Rwork0.1805 --
obs0.1818 107655 95.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.78→43.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4821 0 103 532 5456
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055048
X-RAY DIFFRACTIONf_angle_d0.7216875
X-RAY DIFFRACTIONf_dihedral_angle_d10.4492978
X-RAY DIFFRACTIONf_chiral_restr0.041781
X-RAY DIFFRACTIONf_plane_restr0.004899
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7801-1.80030.47941280.4512481X-RAY DIFFRACTION69
1.8003-1.82150.38551650.41993143X-RAY DIFFRACTION87
1.8215-1.84370.41141780.39443362X-RAY DIFFRACTION94
1.8437-1.8670.43851780.38683367X-RAY DIFFRACTION95
1.867-1.89160.38851780.393395X-RAY DIFFRACTION95
1.8916-1.91750.38751790.37683401X-RAY DIFFRACTION95
1.9175-1.94490.39141840.37243486X-RAY DIFFRACTION97
1.9449-1.97390.3361790.35293390X-RAY DIFFRACTION96
1.9739-2.00480.31971800.34733417X-RAY DIFFRACTION96
2.0048-2.03760.40821810.3743446X-RAY DIFFRACTION96
2.0376-2.07280.35411780.32743390X-RAY DIFFRACTION96
2.0728-2.11050.30671850.31423504X-RAY DIFFRACTION96
2.1105-2.15110.28871780.28223384X-RAY DIFFRACTION96
2.1511-2.1950.26711820.26273460X-RAY DIFFRACTION96
2.195-2.24270.29451800.23733428X-RAY DIFFRACTION96
2.2427-2.29490.26591840.2113495X-RAY DIFFRACTION97
2.2949-2.35230.23351810.19523431X-RAY DIFFRACTION97
2.3523-2.41580.22771840.1813484X-RAY DIFFRACTION97
2.4158-2.48690.21361830.18143496X-RAY DIFFRACTION98
2.4869-2.56720.21361820.1713469X-RAY DIFFRACTION98
2.5672-2.65890.21361830.16763469X-RAY DIFFRACTION98
2.6589-2.76540.18551860.16843532X-RAY DIFFRACTION98
2.7654-2.89120.21871850.1743526X-RAY DIFFRACTION98
2.8912-3.04360.21051850.17663507X-RAY DIFFRACTION98
3.0436-3.23420.18811820.17763461X-RAY DIFFRACTION97
3.2342-3.48390.18091830.16073481X-RAY DIFFRACTION98
3.4839-3.83430.17231840.14193496X-RAY DIFFRACTION98
3.8343-4.38860.15741830.12053481X-RAY DIFFRACTION98
4.3886-5.52740.13381820.12453441X-RAY DIFFRACTION97
5.5274-43.40290.16311820.15033450X-RAY DIFFRACTION96
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)
12.7161-0.04751.43861.31460.76334.22570.03670.1973-0.0145-0.1463-0.13780.01310.0876-0.39850.10390.3057-0.00670.02810.28860.02130.2192-12.5818-7.7522-13.4092
20.32250.32970.13895.54610.51640.17620.01150.0583-0.0923-0.3031-0.0123-0.0660.0074-0.01490.00870.2702-0.01680.00160.3065-0.01060.33579.310228.2117-3.573
33.2222-0.3262-0.98651.61610.94223.9672-0.0926-0.3741-0.0070.1417-0.09640.04390.0012-0.39940.18790.282-0.0144-0.02050.33970.0160.244615.3142.507122.4815
44.8289-4.94613.5065.0535-3.59412.54730.20990.31540.3455-0.4774-0.2668-1.05630.24140.23960.0920.31490.02930.03630.31430.00530.460139.05630.509811.6459
51.49080.2794-0.05695.76270.81961.47540.0055-0.1480.14140.3246-0.05650.0996-0.0018-0.11940.05350.29210.01510.00120.356-0.00780.349135.91450.68113.2619
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 330 )
3X-RAY DIFFRACTION3chain 'B' and (resid 13 through 158 )
4X-RAY DIFFRACTION4chain 'B' and (resid 159 through 185 )
5X-RAY DIFFRACTION5chain 'B' and (resid 186 through 330 )

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