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- PDB-4dzn: A de novo designed Coiled Coil CC-pIL -

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Basic information

Entry
Database: PDB / ID: 4dzn
TitleA de novo designed Coiled Coil CC-pIL
ComponentsCOILED-COIL PEPTIDE CC-PIL
KeywordsDE NOVO PROTEIN
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING, MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsBruning, M. / Thomson, A.R. / Zaccai, N.R. / Brady, R.L. / Woolfson, D.N.
CitationJournal: ACS Synth Biol / Year: 2012
Title: A basis set of de novo coiled-coil Peptide oligomers for rational protein design and synthetic biology.
Authors: Fletcher, J.M. / Boyle, A.L. / Bruning, M. / Bartlett, G.J. / Vincent, T.L. / Zaccai, N.R. / Armstrong, C.T. / Bromley, E.H. / Booth, P.J. / Brady, R.L. / Thomson, A.R. / Woolfson, D.N.
History
DepositionMar 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Advisory / Refinement description / Source and taxonomy
Category: pdbx_entity_src_syn / pdbx_unobs_or_zero_occ_atoms / software
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COILED-COIL PEPTIDE CC-PIL
B: COILED-COIL PEPTIDE CC-PIL
C: COILED-COIL PEPTIDE CC-PIL


Theoretical massNumber of molelcules
Total (without water)10,9503
Polymers10,9503
Non-polymers00
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-38 kcal/mol
Surface area6760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.723, 40.943, 87.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide COILED-COIL PEPTIDE CC-PIL


Mass: 3650.072 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: Solid state peptide synthesis / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.02 Å3/Da / Density % sol: 39.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M NH4H2PO4, 0.1 M Tris, 50% v/v MPD, pH 8.5, 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: Oct 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7 Å / Relative weight: 1
ReflectionResolution: 1.59→43.72 Å / Num. obs: 11991 / % possible obs: 96.1 % / Observed criterion σ(I): 4.6
Reflection shellResolution: 1.6→1.7 Å / % possible all: 95.4

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Processing

Software
NameVersionClassification
ACORNphasing
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: AB INITIO PHASING, MOLECULAR REPLACEMENT
Resolution: 1.59→43.72 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.392 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.088
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19844 573 4.8 %RANDOM
Rwork0.15506 ---
obs0.15714 11348 95.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.405 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å2-0 Å20 Å2
2--0.78 Å2-0 Å2
3----0.92 Å2
Refinement stepCycle: LAST / Resolution: 1.59→43.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms750 0 0 78 828
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022754
X-RAY DIFFRACTIONr_bond_other_d0.0010.02515
X-RAY DIFFRACTIONr_angle_refined_deg1.1152.0641006
X-RAY DIFFRACTIONr_angle_other_deg0.81731277
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.258593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.11427.524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.06215148
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0540.2114
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02795
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02129
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.8778480
X-RAY DIFFRACTIONr_mcbond_other1.8758198
X-RAY DIFFRACTIONr_mcangle_it6.01112740
X-RAY DIFFRACTIONr_scbond_it9.92816274
X-RAY DIFFRACTIONr_scangle_it13.22624266
X-RAY DIFFRACTIONr_rigid_bond_restr2.52631266
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.593→1.634 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 52 -
Rwork0.213 800 -
obs--94.35 %

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