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- PDB-3r4a: Crystal structure of the 4-helix coiled coil CC-tet -

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Basic information

Entry
Database: PDB / ID: 3r4a
TitleCrystal structure of the 4-helix coiled coil CC-tet
Componentscoiled coil helix CC-tet
KeywordsDE NOVO PROTEIN / coiled coil domain / tetramer / KIH interactions / synthetic biology
Biological speciesSynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.0701 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 / Refinement description / Source and taxonomy
Category: pdbx_entity_src_syn / software
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
Revision 1.4Sep 13, 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
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: coiled coil helix CC-tet
B: coiled coil helix CC-tet
C: coiled coil helix CC-tet
D: coiled coil helix CC-tet


Theoretical massNumber of molelcules
Total (without water)13,4524
Polymers13,4524
Non-polymers00
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-54 kcal/mol
Surface area6900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.730, 50.900, 103.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
DetailsTETRAMER CONFIRMED BY ANALYTICAL ULTRACENTRIFUGATION

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Components

#1: Protein/peptide
coiled coil helix CC-tet


Mass: 3363.000 Da / Num. of mol.: 4 / 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.: 63 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.18 Å3/Da / Density % sol: 43.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M lithium sulfate, 0.1M Tris pH 8.5, 1.26M ammonium sulfate, supplemented with 25% 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: I02
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 8, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.07→41.03 Å / Num. obs: 7490 / % possible obs: 100 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 12.8
Reflection shellResolution: 2.07→2.18 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.624 / Mean I/σ(I) obs: 2.9 / % possible all: 99.9

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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: PDB ENTRY 3R4H WITH IODOPHENYL GROUPS CHANGED TO TYROSINE

3r4h


Resolution: 2.0701→22.819 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.17 / σ(F): 0 / Phase error: 24.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2696 362 4.98 %RANDOM
Rwork0.2094 ---
obs0.2123 7271 97.14 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.016 Å2 / ksol: 0.354 e/Å3
Displacement parametersBiso max: 70 Å2 / Biso mean: 29.7758 Å2 / Biso min: 14.43 Å2
Baniso -1Baniso -2Baniso -3
1-0.1044 Å20 Å2-0 Å2
2--8.9886 Å20 Å2
3----9.0929 Å2
Refinement stepCycle: LAST / Resolution: 2.0701→22.819 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms883 0 0 63 946
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007887
X-RAY DIFFRACTIONf_angle_d0.7731182
X-RAY DIFFRACTIONf_dihedral_angle_d18.106334
X-RAY DIFFRACTIONf_chiral_restr0.043143
X-RAY DIFFRACTIONf_plane_restr0.003140
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0701-2.36930.29231140.21442183X-RAY DIFFRACTION94
2.3693-2.98410.30311270.19622281X-RAY DIFFRACTION98
2.9841-22.82010.24681210.21422445X-RAY DIFFRACTION100

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