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- PDB-6owd: Arginine Containing Reengineered Coiled-Coiled Dimer to Examine t... -

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Basic information

Entry
Database: PDB / ID: 6owd
TitleArginine Containing Reengineered Coiled-Coiled Dimer to Examine the Impact of Proximal Cation Identity on Hydrophobically-Driven Assembly
ComponentsR+7
KeywordsDE NOVO PROTEIN / Parallel coiled-coil / Dimer / De novo peptide
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBiok, N.A. / Bingman, C.A. / Gellman, S.H.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)144-481500-4-AAB1263 United States
CitationJournal: Biochemistry / Year: 2019
Title: Retention of Coiled-Coil Dimer Formation in the Absence of Ion Pairing at Positions Flanking the Hydrophobic Core.
Authors: Biok, N.A. / Passow, A.D. / Wang, C. / Bingman, C.A. / Abbott, N.L. / Gellman, S.H.
History
DepositionMay 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: R+7
B: R+7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2667
Polymers7,0882
Non-polymers1775
Water1,13563
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation, Centrifugation showed dimer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.730, 31.290, 23.930
Angle α, β, γ (deg.)90.000, 101.720, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-222-

HOH

21A-227-

HOH

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Components

#1: Protein/peptide R+7


Mass: 3544.177 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

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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: 1.93 Å3/Da / Density % sol: 36.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: No salt, 0.1 M Bis-Tris pH 5.5, 3.0 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1272 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1272 Å / Relative weight: 1
ReflectionResolution: 1.5→36.59 Å / Num. obs: 8381 / % possible obs: 95 % / Redundancy: 6.7 % / Biso Wilson estimate: 32.74 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1088 / Rpim(I) all: 0.04586 / Rrim(I) all: 0.1184 / Net I/σ(I): 12.09
Reflection shellResolution: 1.5→1.554 Å / Redundancy: 7 % / Rmerge(I) obs: 1.003 / Mean I/σ(I) obs: 1.34 / Num. unique obs: 808 / CC1/2: 0.424 / Rpim(I) all: 0.4111 / Rrim(I) all: 1.086 / % possible all: 93.73

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DZM

4dzm


Resolution: 1.5→36.59 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2344 818 9.8 %
Rwork0.184 --
obs-8363 95 %
Displacement parametersBiso mean: 36.62 Å2
Refinement stepCycle: LAST / Resolution: 1.5→36.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms502 0 5 63 570

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