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- PDB-8tm9: Computationally designed tunable C2 symmetric tandem repeat homod... -

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Basic information

Entry
Database: PDB / ID: 8tm9
TitleComputationally designed tunable C2 symmetric tandem repeat homodimer, D_3_633_8x bound to peptide
Components
  • D_3_633_8x peptide bound
  • MC1
KeywordsDE NOVO PROTEIN / homodimer / de novo / designed / cTRP / computational / C2 symmetric / circular tandem repeat protein / cyclic peptide
Function / homologyN-PROPANOL / polypeptide(D)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsKennedy, M.A. / Stoddard, B.L. / Hicks, D.R.
Funding support United States, 5items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DGE-1762114 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM115545 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM139752 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)R01AG063845 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)U19AG065156 United States
CitationJournal: To Be Published
Title: Computationally designed tunable C2 symmetric tandem repeat homodimer, D_3_633_8x bound to peptide
Authors: Kennedy, M.A. / Stoddard, B.L. / Hicks, D.R.
History
DepositionJul 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D_3_633_8x peptide bound
B: D_3_633_8x peptide bound
D: MC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5519
Polymers55,0833
Non-polymers4686
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, Size-exclusion chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-77 kcal/mol
Surface area19530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.717, 54.562, 80.478
Angle α, β, γ (deg.)90.00, 96.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein D_3_633_8x peptide bound


Mass: 27075.873 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: Polypeptide(D) MC1


Mass: 931.170 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-POL / N-PROPANOL / 1-PROPONOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.21 Å3/Da / Density % sol: 44.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.6M ammonium sulfate, 4% 2-Propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 29565 / % possible obs: 99.6 % / Redundancy: 6.3 % / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.031 / Rrim(I) all: 0.081 / Χ2: 0.576 / Net I/σ(I): 5.3 / Num. measured all: 185861
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.05-2.094.80.4214490.9430.9850.1990.4670.4297.6
2.09-2.125.10.38614190.9420.9850.1780.4260.43698
2.12-2.165.30.39114930.930.9820.1810.4330.45399.5
2.16-2.215.50.32714640.9530.9880.150.360.47798.9
2.21-2.265.60.30214650.9550.9890.1390.3330.46899.8
2.26-2.316.10.28714480.9650.9910.1250.3140.4699.3
2.31-2.3760.27414930.9670.9910.1210.30.47799.5
2.37-2.436.50.24214530.9780.9940.1010.2620.48299.8
2.43-2.56.70.23714730.9810.9950.0970.2560.48699.5
2.5-2.586.70.21714710.9820.9960.090.2350.517100
2.58-2.686.60.19914740.9870.9970.0840.2170.51599.8
2.68-2.786.60.16314780.990.9970.0680.1770.52399.9
2.78-2.916.70.13114750.9940.9980.0540.1420.54899.9
2.91-3.066.90.1114840.9950.9990.0450.1190.55399.9
3.06-3.256.90.08814800.9970.9990.0360.0950.60999.9
3.25-3.516.60.07114910.9970.9990.030.0770.642100
3.51-3.866.70.05815060.9970.9990.0240.0630.692100
3.86-4.4270.04914770.9980.9990.020.0530.768100
4.42-5.566.60.04615090.99810.020.050.806100
5.56-506.60.04715630.99910.020.0510.96100

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Processing

Software
NameVersionClassification
PHENIX(1.20rc1_4392: ???)refinement
HKL-2000data scaling
PHASER1.2phasing
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→47.4 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 27.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2484 1987 6.77 %
Rwork0.2096 --
obs0.2122 29347 98.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→47.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3443 0 93 97 3633
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033578
X-RAY DIFFRACTIONf_angle_d0.4774841
X-RAY DIFFRACTIONf_dihedral_angle_d21.326515
X-RAY DIFFRACTIONf_chiral_restr0.033592
X-RAY DIFFRACTIONf_plane_restr0.004600
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.10.30061330.26841820X-RAY DIFFRACTION90
2.1-2.160.2791320.24131884X-RAY DIFFRACTION98
2.16-2.220.30381420.22231934X-RAY DIFFRACTION98
2.22-2.30.27591420.21831942X-RAY DIFFRACTION98
2.3-2.380.26041440.2261968X-RAY DIFFRACTION99
2.38-2.470.291390.22461921X-RAY DIFFRACTION99
2.47-2.590.27921430.2271963X-RAY DIFFRACTION99
2.59-2.720.31671420.24011956X-RAY DIFFRACTION99
2.72-2.890.27381430.22481968X-RAY DIFFRACTION99
2.89-3.120.2561430.22131963X-RAY DIFFRACTION100
3.12-3.430.27041440.22151990X-RAY DIFFRACTION100
3.43-3.920.21011450.18941999X-RAY DIFFRACTION100
3.93-4.940.20371460.18172003X-RAY DIFFRACTION100
4.95-47.40.23971490.2032049X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 10.4471 Å / Origin y: 3.8478 Å / Origin z: 22.1749 Å
111213212223313233
T0.1939 Å20.0194 Å20.0132 Å2-0.2002 Å20.0059 Å2--0.2977 Å2
L1.3245 °20.2345 °2-0.4312 °2-0.4627 °2-0.2173 °2--1.1892 °2
S0.0247 Å °0.1106 Å °0.135 Å °-0.0486 Å °-0.0291 Å °0.0476 Å °-0.115 Å °0.0192 Å °0.0026 Å °
Refinement TLS groupSelection details: all

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