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- PDB-3r4h: Crystal structure of the 4-helix coiled coil CC-Tet-phi22 -

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Basic information

Entry
Database: PDB / ID: 3r4h
TitleCrystal structure of the 4-helix coiled coil CC-Tet-phi22
Componentscoiled coil helix CC-Tet-phi22
KeywordsDE NOVO PROTEIN / coiled coil domain / tetramer / KIH interactions / synthetic biology
Biological speciesSynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7003 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: coiled coil helix CC-Tet-phi22
B: coiled coil helix CC-Tet-phi22
C: coiled coil helix CC-Tet-phi22
D: coiled coil helix CC-Tet-phi22
E: coiled coil helix CC-Tet-phi22
F: coiled coil helix CC-Tet-phi22


Theoretical massNumber of molelcules
Total (without water)20,6996
Polymers20,6996
Non-polymers00
Water73941
1
A: coiled coil helix CC-Tet-phi22
B: coiled coil helix CC-Tet-phi22
C: coiled coil helix CC-Tet-phi22
D: coiled coil helix CC-Tet-phi22


Theoretical massNumber of molelcules
Total (without water)13,7994
Polymers13,7994
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-52 kcal/mol
Surface area6820 Å2
MethodPISA
2
E: coiled coil helix CC-Tet-phi22
F: coiled coil helix CC-Tet-phi22

E: coiled coil helix CC-Tet-phi22
F: coiled coil helix CC-Tet-phi22


Theoretical massNumber of molelcules
Total (without water)13,7994
Polymers13,7994
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+3/21
Buried area4820 Å2
ΔGint-57 kcal/mol
Surface area6710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.840, 84.840, 58.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein/peptide
coiled coil helix CC-Tet-phi22


Mass: 3449.861 Da / Num. of mol.: 6 / Source method: obtained synthetically
Details: Peptide synthesis was carried out according to standard Fmoc SPPS protocols
Source: (synth.) Synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.53 Å3/Da / Density % sol: 51.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Tris pH 7.5, 3M sodium formate, supplemented with 30% glycerol for cryo-protection, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.7 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 13, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7 Å / Relative weight: 1
ReflectionResolution: 2.7→60 Å / Num. obs: 11164 / % possible obs: 100 % / Redundancy: 43.9 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 17
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 45.4 % / Rmerge(I) obs: 0.871 / Mean I/σ(I) obs: 4.9 / % possible all: 100

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
PHENIX1.7_650refinement
SCALAdata scaling
SHELXphasing
DMphasing
CNSrefinement
PDB_EXTRACT3.1data extraction
SHELXSphasing
MOSFLMdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.7003→42.42 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.46 / σ(F): 0 / Phase error: 30.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.27003 520 4.66 %
Rwork0.2008 --
obs0.2042 11164 99.9 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.325 Å2 / ksol: 0.324 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.7069 Å20 Å2-0 Å2
2--8.7069 Å20 Å2
3----17.4139 Å2
Refinement stepCycle: LAST / Resolution: 2.7003→42.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1294 0 0 41 1335
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111294
X-RAY DIFFRACTIONf_angle_d1.3211720
X-RAY DIFFRACTIONf_dihedral_angle_d21.337493
X-RAY DIFFRACTIONf_chiral_restr0.065213
X-RAY DIFFRACTIONf_plane_restr0.003207
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7003-2.9720.4151410.32822665X-RAY DIFFRACTION100
2.972-3.40190.33511210.22932667X-RAY DIFFRACTION100
3.4019-4.28540.29961370.17492655X-RAY DIFFRACTION100
4.2854-42.42520.18511210.18052657X-RAY DIFFRACTION100

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