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- PDB-6s9m: Designed Armadillo Repeat protein Lock2 fused to target peptide K... -

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Basic information

Entry
Database: PDB / ID: 6s9m
TitleDesigned Armadillo Repeat protein Lock2 fused to target peptide KRKRKAKITW
ComponentsLock2_KRKRKAKITW
KeywordsDE NOVO PROTEIN / peptide binder / repeat protein / designed armadillo repeat protein
Function / homologyTRIETHYLENE GLYCOL
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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

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Assembly

Deposited unit
A: Lock2_KRKRKAKITW
B: Lock2_KRKRKAKITW
C: Lock2_KRKRKAKITW
D: Lock2_KRKRKAKITW
E: Lock2_KRKRKAKITW
F: Lock2_KRKRKAKITW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,57643
Polymers189,0146
Non-polymers2,56137
Water19,3121072
1
A: Lock2_KRKRKAKITW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,99111
Polymers31,5021
Non-polymers48910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lock2_KRKRKAKITW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,99111
Polymers31,5021
Non-polymers48910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lock2_KRKRKAKITW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6532
Polymers31,5021
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Lock2_KRKRKAKITW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0918
Polymers31,5021
Non-polymers5897
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Lock2_KRKRKAKITW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1656
Polymers31,5021
Non-polymers6635
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Lock2_KRKRKAKITW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6855
Polymers31,5021
Non-polymers1824
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.853, 85.474, 193.970
Angle α, β, γ (deg.)90.000, 96.320, 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
1020A10 - 309
2020C10 - 309
1030A12 - 308
2030D12 - 308
1040A10 - 308
2040E10 - 308
1050A12 - 308
2050F12 - 308
1060B11 - 308
2060C11 - 308
1070B12 - 308
2070D12 - 308
1080B11 - 308
2080E11 - 308
1090B12 - 308
2090F12 - 308
10100C12 - 308
20100D12 - 308
10110C10 - 308
20110E10 - 308
10120C12 - 308
20120F12 - 308
10130D12 - 308
20130E12 - 308
10140D12 - 309
20140F12 - 309
10150E12 - 308
20150F12 - 308

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

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Lock2_KRKRKAKITW


Mass: 31502.402 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)

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Non-polymers , 5 types, 1109 molecules

#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.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1072 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.41 Å3/Da / Density % sol: 48.88 %
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→48.2 Å / Num. obs: 228033 / % possible obs: 96.3 % / Redundancy: 3.479 % / Biso Wilson estimate: 34.082 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.112 / Rrim(I) all: 0.133 / Χ2: 1.017 / Net I/σ(I): 10.55 / Num. measured all: 793257 / Scaling rejects: 60
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
2-2.053.4230.8711.725778117587168820.6261.03896
2.05-2.113.3020.7132.045357217163162240.70.85494.5
2.11-2.172.9980.5162.614423016463147530.8150.6389.6
2.17-2.243.3780.4463.395167616155153000.8730.53494.7
2.24-2.313.5330.3874.095350515726151460.8990.4696.3
2.31-2.393.5240.3055.365120515057145310.9220.36396.5
2.39-2.483.5330.2736.564996414607141410.9330.32596.8
2.48-2.583.5110.257.294760414027135590.9380.29996.7
2.58-2.73.5790.2378.44671113376130510.9460.28197.6
2.7-2.833.6690.2319.834671012866127320.9570.27299
2.83-2.983.6390.18211.764418312276121410.9720.21498.9
2.98-3.163.5920.14813.384108111585114360.980.17598.7
3.16-3.383.5320.11315.633753510847106260.9880.13598
3.38-3.653.4590.08518.68338841015097970.9930.196.5
3.65-43.1190.05522.2126648924085430.9960.06692.5
4-4.473.4070.04326.4327641844081140.9970.05196.1
4.47-5.163.7650.04327.8927898743174100.9980.0599.7
5.16-6.323.7970.04626.0723647625062270.9980.05499.6
6.32-8.943.7810.03133.6918257483948290.9990.03799.8
8.94-48.23.6760.02440.689525264725910.9990.02897.9

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0189refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→48.2 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 8.503 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.157
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2126 5904 5 %RANDOM
Rwork0.177 ---
obs0.1788 112173 98.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 167.65 Å2 / Biso mean: 32.384 Å2 / Biso min: 12.64 Å2
Baniso -1Baniso -2Baniso -3
1-2.3 Å2-0 Å2-1.03 Å2
2--0.08 Å20 Å2
3----2.1 Å2
Refinement stepCycle: final / Resolution: 2→48.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13207 0 139 1072 14418
Biso mean--64.03 40.04 -
Num. residues----1796
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.01913700
X-RAY DIFFRACTIONr_bond_other_d0.0020.0212969
X-RAY DIFFRACTIONr_angle_refined_deg1.9481.98218574
X-RAY DIFFRACTIONr_angle_other_deg1.079330405
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.29351841
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.38228.462598
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.752152415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.161525
X-RAY DIFFRACTIONr_chiral_restr0.1160.22172
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02115586
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022067
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A186400.07
12B186400.07
21A186120.09
22C186120.09
31A184700.08
32D184700.08
41A185160.08
42E185160.08
51A182720.09
52F182720.09
61B185140.09
62C185140.09
71B185440.08
72D185440.08
81B184920.08
82E184920.08
91B184020.09
92F184020.09
101C182500.09
102D182500.09
111C183560.09
112E183560.09
121C181440.1
122F181440.1
131D185920.08
132E185920.08
141D186820.09
142F186820.09
151E184540.08
152F184540.08
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 433 -
Rwork0.287 8224 -
all-8657 -
obs--97.5 %
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)
10.0728-0.1476-0.05190.31860.0630.29840.01120.0065-0.0064-0.0308-0.0480.01750.03510.01320.03680.02110.00350.03810.0774-0.00640.10451.99223.822347.723
20.0565-0.1339-0.02820.37910.21780.562-0.0130.0173-0.0173-0.009-0.05560.0359-0.04280.02250.06860.0470.01010.02390.03980.00120.102424.667-20.013615.9906
30.2271-0.15170.01670.11340.16252.57820.0220.05490.11280.0139-0.059-0.07390.3598-0.39210.03690.0733-0.07110.01430.11370.01760.057211.6995-15.7734-12.8494
40.13150.17440.17310.3296-0.00690.8055-0.0185-0.01960.0299-0.0378-0.04670.01590.00730.01130.06530.0173-0.0080.03180.06970.00370.12229.7685-28.570352.0062
50.01410.0413-0.05720.23640.10070.8812-0.0032-0.0039-0.00710.0185-0.0306-0.0390.0824-0.03370.03380.0168-0.01930.01830.06510.02150.10588.219714.939177.9339
60.4182-0.05160.38030.29790.08760.5492-0.0740.01160.0603-0.0135-0.0161-0.0030.00490.00790.09010.05720.00490.01640.08250.00770.09895.09868.0796109.2078
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 309
2X-RAY DIFFRACTION2B11 - 309
3X-RAY DIFFRACTION3C10 - 309
4X-RAY DIFFRACTION4D12 - 309
5X-RAY DIFFRACTION5E9 - 309
6X-RAY DIFFRACTION6F12 - 309

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