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- PDB-3r47: Crystal structure of a 6-helix coiled coil CC-hex-H24 -

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Basic information

Entry
Database: PDB / ID: 3r47
TitleCrystal structure of a 6-helix coiled coil CC-hex-H24
Componentscoiled coil helix L24H
KeywordsDE NOVO PROTEIN / coiled coil domain / hexamer / KIH interactions / hydrophobic channel / synthetic biology
Function / homologyBROMIDE ION
Function and homology information
Biological speciesSynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5002 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 1.2Jul 17, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Refinement description / Source and taxonomy
Category: pdbx_entity_src_syn / pdbx_unobs_or_zero_occ_residues ...pdbx_entity_src_syn / pdbx_unobs_or_zero_occ_residues / 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 1.3Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_residues / 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

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Assembly

Deposited unit
A: coiled coil helix L24H
B: coiled coil helix L24H
C: coiled coil helix L24H
E: coiled coil helix L24H
F: coiled coil helix L24H
G: coiled coil helix L24H
H: coiled coil helix L24H
I: coiled coil helix L24H
J: coiled coil helix L24H
K: coiled coil helix L24H
L: coiled coil helix L24H
M: coiled coil helix L24H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,81614
Polymers40,65612
Non-polymers1602
Water2,306128
1
A: coiled coil helix L24H
B: coiled coil helix L24H
C: coiled coil helix L24H
E: coiled coil helix L24H
F: coiled coil helix L24H
G: coiled coil helix L24H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4087
Polymers20,3286
Non-polymers801
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8740 Å2
ΔGint-81 kcal/mol
Surface area9930 Å2
MethodPISA
2
H: coiled coil helix L24H
I: coiled coil helix L24H
J: coiled coil helix L24H
K: coiled coil helix L24H
L: coiled coil helix L24H
M: coiled coil helix L24H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4087
Polymers20,3286
Non-polymers801
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8960 Å2
ΔGint-79 kcal/mol
Surface area9530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.804, 55.804, 139.875
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42

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Components

#1: Protein/peptide
coiled coil helix L24H


Mass: 3387.990 Da / Num. of mol.: 12 / Source method: obtained synthetically
Details: Peptide synthesis was carried out according to standard Fmoc SPPS protocols
Source: (synth.) Synthetic construct (others)
#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.68 Å3/Da / Density % sol: 54.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30mM sodium fluoride, 30 mM sodium bromide, 30 mM sodium iodide, 50 mM sodium HEPES, 50mM MOPS (acid) pH 7.5, 20% PEG-MME 550, 10% PEG 20K, 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: Aug 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→23.9 Å / Num. obs: 14790 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 23.6
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 1.6 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.7_650refinement
PHASERphasing
CNSrefinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3R3K WITH IODOPHENYL GROUPS CHANGED TO TYROSINE

3r3k


Resolution: 2.5002→23.505 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.44 / σ(F): 0 / Phase error: 30.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2847 743 5.05 %
Rwork0.2226 --
obs0.2257 14714 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.42 Å2 / ksol: 0.36 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-32.7804 Å20 Å2-0 Å2
2--32.7804 Å20 Å2
3---14.7803 Å2
Refinement stepCycle: LAST / Resolution: 2.5002→23.505 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2642 0 2 128 2772
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072673
X-RAY DIFFRACTIONf_angle_d0.833564
X-RAY DIFFRACTIONf_dihedral_angle_d17.905996
X-RAY DIFFRACTIONf_chiral_restr0.052411
X-RAY DIFFRACTIONf_plane_restr0.003431
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5002-2.6930.38961540.31122770X-RAY DIFFRACTION100
2.693-2.96360.35691520.25832809X-RAY DIFFRACTION100
2.9636-3.39130.32291610.22852768X-RAY DIFFRACTION100
3.3913-4.26850.25331370.18072830X-RAY DIFFRACTION100
4.2685-23.50570.25851390.23122794X-RAY DIFFRACTION98

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