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- PDB-7qdj: Racemic structure of PK-10 and PK-11 -

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Basic information

Entry
Database: PDB / ID: 7qdj
TitleRacemic structure of PK-10 and PK-11
ComponentsPK-10+PK-11
KeywordsDE NOVO PROTEIN / alpha-helical / Racemic Structure
Function / homologyMALONATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.44 Å
AuthorsKumar, P. / Paterson, N.G. / Woolfson, D.N.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/L01386X/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R00661X/1 United Kingdom
CitationJournal: Nature / Year: 2022
Title: De novo design of discrete, stable 3 10 -helix peptide assemblies.
Authors: Kumar, P. / Paterson, N.G. / Clayden, J. / Woolfson, D.N.
History
DepositionNov 27, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jul 6, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jul 27, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PK-10+PK-11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,2775
Polymers2,0371
Non-polymers2404
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint-4 kcal/mol
Surface area2490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.928, 19.379, 55.644
Angle α, β, γ (deg.)90.000, 96.610, 90.000
Int Tables number15
Space group name H-MC12/c1
Components on special symmetry positions
IDModelComponents
11A-101-

MLI

21A-219-

HOH

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Components

#1: Protein/peptide PK-10+PK-11


Mass: 2036.506 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.77 Å3/Da / Density % sol: 30.53 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.1M (Sodium malonate dibasic monohydrate, Imidazole, Boric acid), 25% w/v PEG1500 at pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9119 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9119 Å / Relative weight: 1
ReflectionResolution: 1.44→27.64 Å / Num. obs: 5150 / % possible obs: 97.1 % / Redundancy: 13 % / CC1/2: 1 / Rmerge(I) obs: 0.032 / Rrim(I) all: 0.034 / Net I/σ(I): 40.8
Reflection shellResolution: 1.44→1.47 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.097 / Mean I/σ(I) obs: 19.1 / Num. unique obs: 305 / CC1/2: 1 / Rrim(I) all: 0.1 / % possible all: 94.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
SHELXTphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.44→15.7 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.187 / SU ML: 0.021 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.051 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1679 230 4.7 %RANDOM
Rwork0.1295 ---
obs0.1314 4677 96.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 40.96 Å2 / Biso mean: 9.84 Å2 / Biso min: 3.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å2-0 Å2-0.21 Å2
2--0.04 Å2-0 Å2
3----0.25 Å2
Refinement stepCycle: final / Resolution: 1.44→15.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms145 0 15 27 187
Biso mean--22.23 19.57 -
Num. residues----21
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.012175
X-RAY DIFFRACTIONr_bond_other_d0.0040.017186
X-RAY DIFFRACTIONr_angle_refined_deg3.2291.658244
X-RAY DIFFRACTIONr_angle_other_deg1.4631.589413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.561522
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.246254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.5141526
X-RAY DIFFRACTIONr_chiral_restr0.160.211
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02628
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02100
X-RAY DIFFRACTIONr_rigid_bond_restr4.8073358
LS refinement shellResolution: 1.44→1.478 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.194 18 -
Rwork0.15 351 -
all-369 -
obs--94.62 %
Refinement TLS params.Method: refined / Origin x: 4.3349 Å / Origin y: 0.9944 Å / Origin z: 2.6809 Å
111213212223313233
T0.0075 Å2-0.0014 Å2-0.0008 Å2-0.0024 Å2-0.0006 Å2--0.0012 Å2
L1.8271 °2-1.5635 °2-2.0332 °2-3.0876 °23.521 °2--7.3728 °2
S-0.0524 Å °-0.0455 Å °0.0251 Å °0.0703 Å °0.0293 Å °0.0152 Å °-0.052 Å °0.1032 Å °0.0232 Å °

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