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- PDB-3r46: Crystal structure of a parallel 6-helix coiled coil CC-hex-D24 -

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Basic information

Entry
Database: PDB / ID: 3r46
TitleCrystal structure of a parallel 6-helix coiled coil CC-hex-D24
Componentscoiled coil helix L24D
KeywordsDE NOVO PROTEIN / coiled coil domain / parallel hexamer / KIH interactions / hydrophobic channel / synthetic biology
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.751 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 1.3Sep 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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 L24D
B: coiled coil helix L24D
C: coiled coil helix L24D
E: coiled coil helix L24D
F: coiled coil helix L24D
G: coiled coil helix L24D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,48013
Polymers21,1696
Non-polymers3127
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8950 Å2
ΔGint-94 kcal/mol
Surface area10220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.176, 55.176, 146.591
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11B-22-

TRP

DetailsHEXAMER CONFIRMED BY ANALYTICAL ULTRACENTRIFUGATION

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Components

#1: Protein/peptide
coiled coil helix L24D


Mass: 3528.104 Da / Num. of mol.: 6 / Source method: obtained synthetically
Details: Peptide synthesis was carried out according to standard Fmoc SPPS protocols
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.64 Å3/Da / Density % sol: 53.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1.5 M sodium chloride, 10% v/v ethanol, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 23735 / % possible obs: 99 % / Redundancy: 23.7 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 37.9
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.576 / Mean I/σ(I) obs: 2.4 / % possible all: 90.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3R3K WITH IODOPHENYL CHANGED TO TRYOSINE

3r3k


Resolution: 1.751→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.126 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1196 5.1 %RANDOM
Rwork0.1993 ---
obs0.201 23338 98.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 73.2 Å2 / Biso mean: 23.6852 Å2 / Biso min: 11.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20 Å20 Å2
2--0.96 Å20 Å2
3----1.92 Å2
Refinement stepCycle: LAST / Resolution: 1.751→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1368 0 17 221 1606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221425
X-RAY DIFFRACTIONr_angle_refined_deg1.4851.9891903
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9865182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.80828.65452
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.53915295
X-RAY DIFFRACTIONr_chiral_restr0.110.2214
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02970
X-RAY DIFFRACTIONr_mcbond_it1.1011.5918
X-RAY DIFFRACTIONr_mcangle_it1.90621420
X-RAY DIFFRACTIONr_scbond_it3.443507
X-RAY DIFFRACTIONr_scangle_it6.0074.5481
LS refinement shellResolution: 1.751→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 81 -
Rwork0.273 1419 -
all-1500 -
obs--88.13 %

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