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- PDB-4j8y: E3_5 DARPin D77S mutant -

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Basic information

Entry
Database: PDB / ID: 4j8y
TitleE3_5 DARPin D77S mutant
ComponentsDARPin_E3_5_D77S
KeywordsDE NOVO PROTEIN / Protein Design / DARPins / ankyrin repeat / unselected DARPin
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: 1.7 Å
AuthorsSeeger, M.A. / Gruetter, M.G.
CitationJournal: Protein Sci. / Year: 2013
Title: Design, construction, and characterization of a second-generation DARPin library with reduced hydrophobicity.
Authors: Seeger, M.A. / Zbinden, R. / Flutsch, A. / Gutte, P.G. / Engeler, S. / Roschitzki-Voser, H. / Grutter, M.G.
History
DepositionFeb 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: DARPin_E3_5_D77S


Theoretical massNumber of molelcules
Total (without water)18,0671
Polymers18,0671
Non-polymers00
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.880, 53.630, 78.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DARPin_E3_5_D77S


Mass: 18067.096 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.03 Å3/Da / Density % sol: 39.37 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 6.5
Details: 1.6 M Na-Citrate, pH 6.5, VAPOR DIFFUSION, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2011
RadiationMonochromator: X06DA / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 16814 / Num. obs: 16705 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.7→1.74 Å / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→44.261 Å / SU ML: 0.16 / σ(F): 1.39 / Phase error: 20.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2067 836 5 %randomly chosen by phenix
Rwork0.1716 ---
obs0.1734 16704 99.35 %-
all-16814 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→44.261 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1173 0 0 167 1340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041212
X-RAY DIFFRACTIONf_angle_d0.8741653
X-RAY DIFFRACTIONf_dihedral_angle_d12.464440
X-RAY DIFFRACTIONf_chiral_restr0.063196
X-RAY DIFFRACTIONf_plane_restr0.005222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.80670.23971370.20922600X-RAY DIFFRACTION99
1.8067-1.94620.22361380.18552620X-RAY DIFFRACTION100
1.9462-2.1420.22431380.16892618X-RAY DIFFRACTION100
2.142-2.45190.21671380.1672624X-RAY DIFFRACTION99
2.4519-3.08910.21551390.18262642X-RAY DIFFRACTION99
3.0891-44.2610.18231460.15852764X-RAY DIFFRACTION99
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)
10.0159-0.03050.00420.0581-0.00950.0029-0.0037-0.00360.00530.07420.0260.0622-0.0109-0.13750.01750.2703-0.06320.20150.2064-0.0071-0.0065-24.0846-12.792622.2266
20.00370.01040.00280.02920.00860.0047-0.0520.0133-0.03210.0047-0.0157-0.02920.06680.0224-0.05390.56-0.1290.14540.23820.10630.1494-19.197-20.682522.8635
30.1379-0.03370.0390.17860.09050.25550.0464-0.11950.04260.15270.03090.13380.0574-0.05170.08250.113-0.04480.04680.14720.01980.0757-21.3022-11.306515.1848
40.01370.0299-0.04490.0709-0.120.2295-0.0344-0.0649-0.075-0.0144-0.0591-0.07080.0760.0787-0.07870.2391-0.00830.00660.06380.10320.0295-13.8629-19.747714.6733
50.34850.0995-0.26240.1995-0.09730.20030.1178-0.02180.14620.0979-0.00150.0845-0.0116-0.08490.08390.0487-0.0157-0.00310.08820.00010.0768-15.5666-6.98178.1392
60.00350.00610.00270.0116-0.01010.044-0.0389-0.186-0.1386-0.0409-0.1198-0.1261-0.00380.1608-0.01710.0730.00420.00220.10870.03090.0954-6.6242-13.39548.3686
70.00020.006-0.00330.0674-0.08860.1198-0.01340.17870.09720.01220.06390.06060.0147-0.15470.00450.0860.02070.00960.11220.03320.1305-15.243-4.13120.6451
80.02620.0468-0.02460.084-0.04760.02740.0434-0.02530.1283-0.0760.0829-0.0616-0.0594-0.00160.0110.0620.00440.01010.0924-0.02780.1144-7.68981.96026.2688
90.0098-0.00830.04220.0752-0.03930.18150.0264-0.10980.0037-0.0458-0.0153-0.09190.02290.10550.0218-0.0290.0320.0090.1062-0.01950.1628-0.2541-4.514.762
100.0094-0.01290.00750.02830.01310.02110.04240.0390.1894-0.00790.05170.0923-0.1722-0.06720.10950.17380.06140.03630.07890.0390.164-8.99632.1918-3.2206
110.0266-0.002-0.00470.00140.00440.09140.0538-0.00160.09810.0813-0.01-0.2064-0.2120.08460.00650.1527-0.03030.0230.11290.00740.2984-1.51088.83783.5405
120.00070.0004-0.00140-0.00080.00130.0110.0450.0091-0.05350.0465-0.0288-0.0080.02340.00010.2495-0.02660.11680.42-00.47633.14344.2568-3.8896
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 13:25)
2X-RAY DIFFRACTION2(chain A and resid 26:34)
3X-RAY DIFFRACTION3(chain A and resid 35:60)
4X-RAY DIFFRACTION4(chain A and resid 61:69)
5X-RAY DIFFRACTION5(chain A and resid 70:93)
6X-RAY DIFFRACTION6(chain A and resid 94:101)
7X-RAY DIFFRACTION7(chain A and resid 102:114)
8X-RAY DIFFRACTION8(chain A and resid 115:125)
9X-RAY DIFFRACTION9(chain A and resid 126:133)
10X-RAY DIFFRACTION10(chain A and resid 134:147)
11X-RAY DIFFRACTION11(chain A and resid 148:163)
12X-RAY DIFFRACTION12(chain A and resid 164:169)

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