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- PDB-6sa7: DARPin-Armadillo fusion C8long83 -

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Basic information

Entry
Database: PDB / ID: 6sa7
TitleDARPin-Armadillo fusion C8long83
ComponentsDARPin-Armadillo fusion C8long83
KeywordsDE NOVO PROTEIN / protein fusion / DARPin / Armadillo / shared helix / crystallization chaperone
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: 3.3 Å
AuthorsErnst, P. / Honegger, A. / van der Valk, F. / Ewald, C. / Mittl, P.R.E. / Plucktun, A.
CitationJournal: Sci Rep / Year: 2019
Title: Rigid fusions of designed helical repeat binding proteins efficiently protect a binding surface from crystal contacts.
Authors: Ernst, P. / Honegger, A. / van der Valk, F. / Ewald, C. / Mittl, P.R.E. / Pluckthun, A.
History
DepositionJul 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DARPin-Armadillo fusion C8long83
B: DARPin-Armadillo fusion C8long83


Theoretical massNumber of molelcules
Total (without water)107,9472
Polymers107,9472
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint3 kcal/mol
Surface area44210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.470, 167.540, 95.030
Angle α, β, γ (deg.)90.000, 97.930, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: LYS / End label comp-ID: LYS / Label seq-ID: 5 - 507

Dom-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1chain AAA5 - 507
2chain BBB5 - 509

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Components

#1: Protein DARPin-Armadillo fusion C8long83


Mass: 53973.582 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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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: 4.05 Å3/Da / Density % sol: 69.65 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 4.3 M NaCl 0.1M HEPES NaOH pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99999815963 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999815963 Å / Relative weight: 1
ReflectionResolution: 3.3→48.03 Å / Num. obs: 24183 / % possible obs: 95.2 % / Redundancy: 7.44 % / Biso Wilson estimate: 85.798 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.216 / Rrim(I) all: 0.233 / Χ2: 0.785 / Net I/σ(I): 6.75
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3.3-3.397.7231.9861.0318640.4072.12899.1
3.39-3.487.6791.4141.4617180.5631.51695.8
3.48-3.587.6920.9882.2117970.7361.0699.7
3.58-3.697.5140.8552.5716140.7860.91894.3
3.69-3.817.5320.5993.6316660.8980.64399.9
3.81-3.947.5230.4694.515440.9380.50494.5
3.94-4.097.4960.3955.2215190.950.42597
4.09-4.267.3350.3345.9914440.9590.3697
4.26-4.457.3640.2447.4413760.9810.26295.5
4.45-4.677.2220.2258.1513090.9780.24393.9
4.67-4.927.3470.2288.4512430.9820.24694.7
4.92-5.227.3430.3127.3311380.9660.33792.4
5.22-5.587.3750.38.1210470.9680.32489.3
5.58-6.027.2840.2319.668560.9720.2577.8
6.02-6.67.3690.20610.468520.9740.22387.2
6.6-7.387.3380.14213.449200.9870.15399.6
7.38-8.527.2320.08817.427920.9950.09599.2
8.52-10.447.0740.06819.666780.9960.07499.3
10.44-14.767.070.0719.945260.9950.07698.7
14.76-48.036.950.07520.532800.9910.08194.3

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→48.03 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.5
RfactorNum. reflection% reflection
Rfree0.2762 1208 5 %
Rwork0.2327 --
obs0.2348 24154 95.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 546.48 Å2 / Biso mean: 135.0186 Å2 / Biso min: 47.61 Å2
Refinement stepCycle: final / Resolution: 3.3→48.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7458 0 0 0 7458
Num. residues----998
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4422X-RAY DIFFRACTION6.343TORSIONAL
12B4422X-RAY DIFFRACTION6.343TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.3-3.43210.38171380.3726263098
3.4321-3.58820.35721370.3144260298
3.5882-3.77740.29341360.2826258497
3.7774-4.01390.28271360.2403257897
4.0139-4.32360.32171340.2425255196
4.3236-4.75840.30771350.2216256795
4.7584-5.44610.28381300.2364246192
5.4461-6.85830.2771210.2501230985
6.8583-48.030.20471410.1752266499
Refinement TLS params.Method: refined / Origin x: -15.3151 Å / Origin y: 24.3026 Å / Origin z: -16.4565 Å
111213212223313233
T0.5679 Å2-0.0052 Å20.0068 Å2-0.6936 Å2-0.0021 Å2--0.7153 Å2
L0.1102 °2-0.1789 °2-0.0074 °2-0.3148 °2-0.059 °2--0.5591 °2
S0.0096 Å °-0.0877 Å °0.029 Å °0.2103 Å °-0.0266 Å °0.0713 Å °-0.0414 Å °0.0142 Å °0.0119 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA5 - 507
2X-RAY DIFFRACTION1allB5 - 509

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