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- PDB-6s9l: Designed Armadillo Repeat protein Lock1 bound to (KR)4KLSF target -

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Basic information

Entry
Database: PDB / ID: 6s9l
TitleDesigned Armadillo Repeat protein Lock1 bound to (KR)4KLSF target
Components
  • KR4KLSF Lock1
  • LYS-ARG-LYS-ARG-LYS-ARG-LYS-ARG-LYS-LEU-SER-PHE
KeywordsDE NOVO PROTEIN / peptide binder / repeat protein / designed armadillo repeat protein
Function / homologyLeucine-rich Repeat Variant / Leucine-rich Repeat Variant / Alpha Horseshoe / Mainly Alpha
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsErnst, P. / Zosel, F. / Reichen, C. / Schuler, B. / Pluckthun, A.
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Structure-Guided Design of a Peptide Lock for Modular Peptide Binders.
Authors: Ernst, P. / Zosel, F. / Reichen, C. / Nettels, D. / Schuler, B. / Pluckthun, A.
History
DepositionJul 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2May 15, 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: KR4KLSF Lock1
B: KR4KLSF Lock1
C: LYS-ARG-LYS-ARG-LYS-ARG-LYS-ARG-LYS-LEU-SER-PHE
D: LYS-ARG-LYS-ARG-LYS-ARG-LYS-ARG-LYS-LEU-SER-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,87611
Polymers63,0494
Non-polymers8277
Water5,350297
1
A: KR4KLSF Lock1
C: LYS-ARG-LYS-ARG-LYS-ARG-LYS-ARG-LYS-LEU-SER-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9976
Polymers31,5242
Non-polymers4734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-26 kcal/mol
Surface area12520 Å2
MethodPISA
2
B: KR4KLSF Lock1
D: LYS-ARG-LYS-ARG-LYS-ARG-LYS-ARG-LYS-LEU-SER-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8795
Polymers31,5242
Non-polymers3553
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-20 kcal/mol
Surface area12460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.350, 80.260, 122.720
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein KR4KLSF Lock1


Mass: 29884.352 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)
#2: Protein/peptide LYS-ARG-LYS-ARG-LYS-ARG-LYS-ARG-LYS-LEU-SER-PHE


Mass: 1640.099 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.33 Å3/Da / Density % sol: 47.23 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / Details: 0.1M HEPES/NaOH pH 8 66% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→48.75 Å / Num. obs: 66103 / % possible obs: 100 % / Redundancy: 7.148 % / Biso Wilson estimate: 32.526 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.355 / Rrim(I) all: 0.383 / Χ2: 0.802 / Net I/σ(I): 4.98
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
2.1-2.157.3282.380.8835774488348820.3142.56100
2.15-2.217.2791.9171.1234838478747860.3822.063100
2.21-2.287.2571.6851.2533852466646650.4651.814100
2.28-2.357.2211.3831.5432351448244800.5451.49100
2.35-2.427.21.1551.8431415436343630.6111.244100
2.42-2.517.1831.012.0430608426142610.6871.088100
2.51-2.67.190.9042.2829048404240400.7220.974100
2.6-2.717.1530.782.6828011391939160.7840.8499.9
2.71-2.836.9930.6313.1926118373637350.8280.682100
2.83-2.976.8110.4963.9524644361836180.8910.537100
2.97-3.136.3440.3834.7621582340234020.9260.417100
3.13-3.326.0990.3085.6619840325332530.9420.337100
3.32-3.556.6250.2457.2620015302130210.970.266100
3.55-3.836.9250.1710.1219598283028300.9840.184100
3.83-4.27.8730.13613.2220446259725970.9910.146100
4.2-4.77.8780.11615.1218457234323430.9940.124100
4.7-5.427.870.14312.4116299207120710.9920.153100
5.42-6.647.8490.15511.7213790175717570.9880.166100
6.64-9.397.7490.08918.9310368133813380.9960.096100
9.39-48.7467.3290.06723.2154607487450.9970.07299.6

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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: 2.1→48.75 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.83
RfactorNum. reflection% reflection
Rfree0.2363 1749 5 %
Rwork0.2071 --
obs0.2086 34964 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 95.73 Å2 / Biso mean: 33.8657 Å2 / Biso min: 10.58 Å2
Refinement stepCycle: final / Resolution: 2.1→48.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4409 0 56 297 4762
Biso mean--55.89 37.25 -
Num. residues----592
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.1001-2.16190.35251440.30242726
2.1619-2.23160.32911440.2822740
2.2316-2.31140.30281430.27782717
2.3114-2.40390.26341440.24782727
2.4039-2.51340.28131440.23712737
2.5134-2.64590.26981420.23632716
2.6459-2.81160.2551460.22362770
2.8116-3.02870.26791450.21562741
3.0287-3.33340.20761470.20032792
3.3334-3.81560.23461450.17732767
3.8156-4.80660.1771490.15752823
4.8066-48.750.19371560.18332959
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)
10.83930.22150.19450.98550.64622.3012-0.0178-0.1033-0.07850.17270.0177-0.01020.26470.0281-0.01920.13880.01180.01770.15590.04360.19816.909291.340122.586
21.9943-0.00660.20161.60160.42910.95450.0395-0.07430.08690.02670.0252-0.0999-0.0672-0.0812-0.0430.12040.01840.03290.14520.01680.1543-6.118111.592116.4166
33.3596-0.42461.29764.14290.39827.61910.088-0.0103-0.3457-0.2171-0.10840.1470.7291-0.36930.03410.2196-0.01030.01160.3032-0.02380.293110.217790.87726.0282
42.8130.43230.1626.62173.30123.92080.1009-0.3540.2755-0.2924-0.1061-0.1233-0.6854-0.11650.0570.28440.01260.00520.20890.00470.2433-8.4372115.56429.8841
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 9:293)A9 - 293
2X-RAY DIFFRACTION2(chain B and resseq 10:292)B10 - 292
3X-RAY DIFFRACTION3(chain C and resseq 1:12)C1 - 12
4X-RAY DIFFRACTION4(chain D and resseq 1:12)D1 - 12

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