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- PDB-6sa8: ring-like DARPin-Armadillo fusion H83_D01 -

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Basic information

Entry
Database: PDB / ID: 6sa8
Titlering-like DARPin-Armadillo fusion H83_D01
Components
  • LYS-ARG-LYS-ARG-LYS-ARG-LYS-ARG-LYS-ARG
  • ring-like DARPin-Armadillo fusion H83_D01
KeywordsDE NOVO PROTEIN / protein fusion / DARPin / Armadillo / shared helix / crystallization chaperone
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ring-like DARPin-Armadillo fusion H83_D01
B: LYS-ARG-LYS-ARG-LYS-ARG-LYS-ARG-LYS-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9783
Polymers71,9162
Non-polymers621
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint12 kcal/mol
Surface area29020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.970, 145.460, 115.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein ring-like DARPin-Armadillo fusion H83_D01


Mass: 70466.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Protein/peptide LYS-ARG-LYS-ARG-LYS-ARG-LYS-ARG-LYS-ARG


Mass: 1449.883 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 25 % PEG 2000 MME 0.2 M MgCl2 0.1M Tris HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00000050167 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00000050167 Å / Relative weight: 1
ReflectionResolution: 2.4→46.5 Å / Num. obs: 30897 / % possible obs: 99.7 % / Redundancy: 25.203 % / Biso Wilson estimate: 63.831 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.369 / Rrim(I) all: 0.377 / Χ2: 0.974 / Net I/σ(I): 12.34
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.4-2.4627.6014.4951.1262296225722570.5414.579100
2.46-2.5327.5634.0941.3560915221022100.7274.171100
2.53-2.627.3873.5141.6758554214121380.7043.58199.9
2.6-2.6819.4864.1630.7840472207720770.3614.281100
2.68-2.7726.2282.9452.1353506204120400.8223.003100
2.77-2.8724.5511.9873.5248047195819570.8972.02999.9
2.87-2.9826.1151.4215.0649593189918990.9341.449100
2.98-3.128.1961.1036.951767183618360.9591.123100
3.1-3.2428.0210.9178.5348533173217320.9780.934100
3.24-3.3927.5450.839.545615166516560.9790.84699.5
3.39-3.5821.3550.6149.4334617162116210.9740.63100
3.58-3.7920.0180.49912.2429666151714820.9780.51297.7
3.79-4.0619.7570.36517.4427206142713770.9850.37596.5
4.06-4.3823.0530.23129.6530730133313330.9970.236100
4.38-4.826.7380.19535.4433289124512450.9990.199100
4.8-5.3727.2230.20433.1930245111111110.9990.208100
5.37-6.226.4920.19932.4726598100410040.9990.203100
6.2-7.5924.660.12541.86209368498490.9990.127100
7.59-10.7324.0740.07454.361629867767710.076100
10.73-46.51524.7950.06859.4498194013960.9990.06998.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→46.5 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 32.29
RfactorNum. reflection% reflection
Rfree0.2746 1543 5.01 %
Rwork0.2375 --
obs0.2394 30805 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 211.36 Å2 / Biso mean: 82.5086 Å2 / Biso min: 34.55 Å2
Refinement stepCycle: final / Resolution: 2.4→46.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5034 0 4 111 5149
Biso mean--92.31 58.7 -
Num. residues----675
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4-2.47750.34031380.30762627100
2.4775-2.5660.34431400.31052646100
2.566-2.66870.44831390.4037258798
2.6687-2.79020.43921370.3501261699
2.7902-2.93730.28411390.26742643100
2.9373-3.12130.32241400.25482666100
3.1213-3.36220.32111410.27162668100
3.3622-3.70040.3451380.2843263798
3.7004-4.23560.26751400.2232264898
4.2356-5.33520.22541420.19612702100
5.3352-46.50.20271490.17922822100
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)
18.2974-0.2591-0.86510.8266-0.48051.3782-0.39060.5445-1.7471-0.2-0.1833-0.83120.58320.56650.3920.8686-0.00090.27181.07210.12841.6377-5.7955-12.9326-12.8973
23.6562.8335-0.59613.123-0.39190.2064-0.0928-0.1061-0.07810.01660.1343-0.12580.06520.0088-0.04570.3706-0.042-0.02240.5699-0.00380.2932-23.672725.0233-8.2132
34.1667-2.9155-2.56182.272.1121.9183-0.15120.0345-0.04710.10330.02580.11550.33410.13050.13650.41420.0072-0.04540.50490.03420.351512.197730.4839-15.0297
43.4151-1.92970.69618.2306-3.94424.37190.38210.031-0.5414-0.5151-0.22530.04050.6016-0.0084-0.15410.41540.0946-0.06460.6180.06260.44633.50250.2232-16.5682
56.59232.57292.93616.0908-1.62567.61071.2433-1.03590.3390.8044-0.8359-0.2882-0.4151.2269-0.56180.6132-0.03460.04780.8347-0.05610.8985-9.058724.403-13.4485
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 188 )A7 - 188
2X-RAY DIFFRACTION2chain 'A' and (resid 189 through 401 )A189 - 401
3X-RAY DIFFRACTION3chain 'A' and (resid 402 through 537 )A402 - 537
4X-RAY DIFFRACTION4chain 'A' and (resid 538 through 671 )A538 - 671
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 12 )B1 - 12

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