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- PDB-3r48: Crystal structure of a hetero-hexamer coiled coil -

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Basic information

Entry
Database: PDB / ID: 3r48
TitleCrystal structure of a hetero-hexamer coiled coil
Components
  • coiled coil helix W22-L24H
  • coiled coil helix Y15-L24D
KeywordsDE NOVO PROTEIN / coiled coil domain / hexamer / KIH interactions / hydrophobic channel / synthetic biology
Biological speciesSynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.0011 Å
AuthorsZaccai, N.R. / Chi, B.H.C. / Woolfson, D.N. / Brady, R.L.
CitationJournal: Nat.Chem.Biol. / Year: 2011
Title: A de novo peptide hexamer with a mutable channel.
Authors: Zaccai, N.R. / Chi, B. / Thomson, A.R. / Boyle, A.L. / Bartlett, G.J. / Bruning, M. / Linden, N. / Sessions, R.B. / Booth, P.J. / Brady, R.L. / Woolfson, D.N.
History
DepositionMar 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2011Group: Database references
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Source and taxonomy
Category: pdbx_entity_src_syn / software / struct_conn
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific ..._pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: coiled coil helix W22-L24H
B: coiled coil helix Y15-L24D
C: coiled coil helix Y15-L24D
E: coiled coil helix Y15-L24D
F: coiled coil helix W22-L24H
G: coiled coil helix W22-L24H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8977
Polymers19,8056
Non-polymers921
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9330 Å2
ΔGint-83 kcal/mol
Surface area10050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.872, 50.850, 31.681
Angle α, β, γ (deg.)90.00, 91.05, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-227-

HOH

DetailsHEXAMER CONFIRMED BY ANALYTICAL CENTRIFUGATION

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Components

#1: Protein/peptide coiled coil helix W22-L24H


Mass: 3387.990 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: Peptide synthesis was carried out according to standard Fmoc SPPS protocols
Source: (synth.) Synthetic construct (others)
#2: Protein/peptide coiled coil helix Y15-L24D


Mass: 3213.765 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: Peptide synthesis was carried out according to standard Fmoc SPPS protocols
Source: (synth.) Synthetic construct (others)
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 3.03 Å3/Da / Density % sol: 59.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M sodium chloride, 0.1M sodium/potassium phosphate pH 6.5, 25% w/v PEG 1000, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 14338 / % possible obs: 88.9 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 16
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 1.8 / % possible all: 46.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.7_650refinement
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SEMI-REFINED PDB ENTRY 3R46

3r46


Resolution: 2.0011→37.212 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.33 / σ(F): 0 / Phase error: 32.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2768 714 4.99 %
Rwork0.2098 --
obs0.2132 14303 88.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.526 Å2 / ksol: 0.346 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--11.305 Å20 Å24.8204 Å2
2--22.8059 Å20 Å2
3----7.0424 Å2
Refinement stepCycle: LAST / Resolution: 2.0011→37.212 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1378 0 6 164 1548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151553
X-RAY DIFFRACTIONf_angle_d0.8541860
X-RAY DIFFRACTIONf_dihedral_angle_d15.89533
X-RAY DIFFRACTIONf_chiral_restr0.058215
X-RAY DIFFRACTIONf_plane_restr0.003229
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0011-2.15560.3556780.26911643X-RAY DIFFRACTION54
2.1556-2.37250.33151440.23412735X-RAY DIFFRACTION90
2.3725-2.71580.28941550.2233054X-RAY DIFFRACTION100
2.7158-3.42120.27551590.21483063X-RAY DIFFRACTION100
3.4212-37.21810.25441780.18923094X-RAY DIFFRACTION99

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