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- PDB-6s9n: Designed Armadillo Repeat protein Lock2 fused to target peptide K... -

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Basic information

Entry
Database: PDB / ID: 6s9n
TitleDesigned Armadillo Repeat protein Lock2 fused to target peptide KRKRKAKLSF
ComponentsLock2_KRKRKAKLSF
KeywordsDE NOVO PROTEIN / peptide binder / repeat protein / designed armadillo repeat protein
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lock2_KRKRKAKLSF
B: Lock2_KRKRKAKLSF
C: Lock2_KRKRKAKLSF
D: Lock2_KRKRKAKLSF
E: Lock2_KRKRKAKLSF
F: Lock2_KRKRKAKLSF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,48025
Polymers188,6966
Non-polymers78319
Water21,1501174
1
A: Lock2_KRKRKAKLSF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6907
Polymers31,4491
Non-polymers2406
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lock2_KRKRKAKLSF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6506
Polymers31,4491
Non-polymers2005
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lock2_KRKRKAKLSF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6907
Polymers31,4491
Non-polymers2406
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Lock2_KRKRKAKLSF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4892
Polymers31,4491
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Lock2_KRKRKAKLSF


Theoretical massNumber of molelcules
Total (without water)31,4491
Polymers31,4491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Lock2_KRKRKAKLSF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5112
Polymers31,4491
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.260, 85.500, 194.030
Angle α, β, γ (deg.)90.000, 96.330, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A11 - 308
2010B11 - 308
1020A11 - 308
2020C11 - 308
1030A11 - 308
2030D11 - 308
1040A10 - 308
2040E10 - 308
1050A11 - 308
2050F11 - 308
1060B11 - 309
2060C11 - 309
1070B11 - 309
2070D11 - 309
1080B11 - 308
2080E11 - 308
1090B11 - 309
2090F11 - 309
10100C11 - 309
20100D11 - 309
10110C11 - 308
20110E11 - 308
10120C11 - 309
20120F11 - 309
10130D11 - 308
20130E11 - 308
10140D11 - 309
20140F11 - 309
10150E11 - 308
20150F11 - 308

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Lock2_KRKRKAKLSF


Mass: 31449.340 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 1174 / 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: 2.43 Å3/Da / Density % sol: 49.34 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion
Details: 22.5 % PEG smear medium 0.1 M CaCl2, 0.1 M MgCl2, 0.1 M Pipes pH 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.000041 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000041 Å / Relative weight: 1
ReflectionResolution: 2.1→45.61 Å / Num. obs: 199596 / % possible obs: 96.8 % / Redundancy: 2.793 % / Biso Wilson estimate: 34.209 Å2 / CC1/2: 0.972 / Rmerge(I) obs: 0.213 / Rrim(I) all: 0.264 / Χ2: 0.902 / Net I/σ(I): 4.89 / Num. measured all: 557469 / Scaling rejects: 1136
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
2.1-2.152.3750.9980.963412915244143710.5071.25294.3
2.15-2.212.5320.8641.23670914972144960.6171.07296.8
2.21-2.282.8630.8011.434062314353141880.6750.97598.9
2.28-2.352.8610.6541.743948213974137980.7460.79798.7
2.35-2.422.8630.5412.113877013722135420.7980.6698.7
2.42-2.512.8650.4672.43683713164128590.8620.57297.7
2.51-2.62.8660.4352.623560712695124240.8540.53297.9
2.6-2.712.8990.4252.833433112142118420.8510.5297.5
2.71-2.832.8580.3423.43254311779113860.8970.4296.7
2.83-2.972.8460.294.043027311178106360.9130.35895.2
2.97-3.132.8470.2674.852892910596101600.9220.3395.9
3.13-3.322.8130.2326.04274001013697390.9290.2996.1
3.32-3.552.7660.1977.3725127944890840.9280.24796.1
3.55-3.832.6580.1569.3322137878483300.940.19894.8
3.83-4.22.4070.12410.7118102814075200.9560.15892.4
4.2-4.73.0310.10614.221763732871800.9730.13198
4.7-5.423.0610.12412.4819587646763980.9690.15498.9
5.42-6.643.0570.12711.7116459545553840.9660.15898.7
6.64-9.393.0180.06716.8612452423141260.9930.08397.5
9.39-45.612.9110.05421.076209228921330.9940.06693.2

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0189refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→45.61 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.917 / SU B: 15.527 / SU ML: 0.205 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.287 / ESU R Free: 0.216
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2616 5177 5 %RANDOM
Rwork0.2234 ---
obs0.2253 98361 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 113 Å2 / Biso mean: 33.651 Å2 / Biso min: 11.79 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å2-0 Å2-1.01 Å2
2---0.72 Å20 Å2
3----0.27 Å2
Refinement stepCycle: final / Resolution: 2.1→45.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13191 0 22 1174 14387
Biso mean--38.2 40.38 -
Num. residues----1797
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01913444
X-RAY DIFFRACTIONr_bond_other_d0.0020.0212674
X-RAY DIFFRACTIONr_angle_refined_deg1.81.98118259
X-RAY DIFFRACTIONr_angle_other_deg1.066329718
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.14951815
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.03428.583593
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.992152384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3261521
X-RAY DIFFRACTIONr_chiral_restr0.1090.22155
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02115362
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022020
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A184600.08
12B184600.08
21A182940.09
22C182940.09
31A182940.08
32D182940.08
41A182420.09
42E182420.09
51A181360.09
52F181360.09
61B185480.08
62C185480.08
71B184620.08
72D184620.08
81B183400.08
82E183400.08
91B183560.09
92F183560.09
101C185280.08
102D185280.08
111C184040.08
112E184040.08
121C185000.09
122F185000.09
131D182840.08
132E182840.08
141D182860.09
142F182860.09
151E181300.09
152F181300.09
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 369 -
Rwork0.341 7010 -
all-7379 -
obs--95.82 %
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)
10.04850.1195-0.07410.3824-0.03710.35580.0003-0.0131-0.00980.0275-0.0291-0.01510.041-0.00350.02880.28320.00790.09760.24620.00950.0358-2.091235.6265-47.7333
20.08850.166-0.04180.3636-0.22720.5648-0.0105-0.0018-0.00970.0176-0.0482-0.0244-0.04070.00240.05860.32790.00650.10030.2210.00260.0395-24.8031-8.2806-16.0646
30.2809-0.2080.28390.28120.00350.6473-0.0050.01390.02240.0016-0.0212-0.011-0.0315-0.00810.02620.30060.00250.11690.2562-0.00330.0482-30.0312-16.7742-52.0557
40.2085-0.1551-0.00790.1280.13641.72180.01220.07540.05440.0294-0.0581-0.03150.1665-0.22060.04580.3434-0.0250.07610.29990.01490.029911.632338.8608-12.8961
50.011-0.018-0.07440.2061-0.10750.8038-0.0097-0.008-0.008-0.0268-0.00040.04360.09980.04560.01010.32720.02130.09450.2406-0.01290.042-8.296526.7378-78.0131
60.5301-0.02090.53990.15540.08380.6417-0.06940.020.036-0.03850.0301-0.0265-0.0230.01860.03930.33110.00240.09920.25020.0120.0373-28.6275-22.9539-83.6393
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 309
2X-RAY DIFFRACTION2B11 - 309
3X-RAY DIFFRACTION3C11 - 309
4X-RAY DIFFRACTION4D11 - 309
5X-RAY DIFFRACTION5E9 - 309
6X-RAY DIFFRACTION6F11 - 309

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