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- PDB-7arr: The de novo designed hybrid alpha/beta-miniprotein -

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Basic information

Entry
Database: PDB / ID: 7arr
TitleThe de novo designed hybrid alpha/beta-miniprotein
Componentsalpha/beta-peptide
KeywordsDE NOVO PROTEIN / alpha/beta-peptide / foldamer
Function / homologytrifluoroacetic acid
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsBejger, M. / Fortuna, P. / Drewniak-Switalska, M. / Rypniewski, W. / Berlicki, L.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science CentreDEC-2016/21/B/ST5/00269 Poland
CitationJournal: Chem.Commun.(Camb.) / Year: 2021
Title: A computationally designed beta-amino acid-containing miniprotein.
Authors: Bejger, M. / Fortuna, P. / Drewniak-Switalska, M. / Plewka, J. / Rypniewski, W. / Berlicki, L.
History
DepositionOct 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: alpha/beta-peptide
B: alpha/beta-peptide
C: alpha/beta-peptide
D: alpha/beta-peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5499
Polymers16,3264
Non-polymers2225
Water5,368298
1
A: alpha/beta-peptide
D: alpha/beta-peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3616
Polymers8,1632
Non-polymers1984
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-27 kcal/mol
Surface area4670 Å2
MethodPISA
2
B: alpha/beta-peptide
C: alpha/beta-peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1883
Polymers8,1632
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-15 kcal/mol
Surface area4530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.937, 32.068, 43.087
Angle α, β, γ (deg.)114.160, 91.880, 109.860
Int Tables number1
Space group name H-MP1

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Components

#1: Protein/peptide
alpha/beta-peptide


Mass: 4081.618 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-TFA / trifluoroacetic acid


Mass: 114.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2HF3O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.28 Å3/Da / Density % sol: 46.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M magnesium chloride hexahydrate 0.1 M HEPES pH 7.5 25 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97626 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. obs: 49390 / % possible obs: 87.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 15.1 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.027 / Net I/σ(I): 24.5
Reflection shellResolution: 1.1→1.17 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 7.34 / Num. unique obs: 7297 / CC1/2: 0.98 / % possible all: 80.1

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: not deposited

Resolution: 1.1→29.02 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.174 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.032 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1607 998 2 %RANDOM
Rwork0.1293 ---
obs0.1299 48389 87.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 101.16 Å2 / Biso mean: 14.162 Å2 / Biso min: 6.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20.69 Å2-0.63 Å2
2--0.37 Å2-0.82 Å2
3---0.43 Å2
Refinement stepCycle: final / Resolution: 1.1→29.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1110 0 19 310 1439
Biso mean--16.5 29.68 -
Num. residues----136
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0141283
X-RAY DIFFRACTIONr_bond_other_d0.0030.0181218
X-RAY DIFFRACTIONr_angle_refined_deg2.7621.7891714
X-RAY DIFFRACTIONr_angle_other_deg1.6431.742919
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8075130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.24625.87363
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.27815256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.512154
X-RAY DIFFRACTIONr_chiral_restr0.1520.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021255
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02198
X-RAY DIFFRACTIONr_rigid_bond_restr10.58432493
LS refinement shellResolution: 1.1→1.129 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.209 64 -
Rwork0.194 3123 -
all-3187 -
obs--76.83 %

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