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- PDB-4dzk: A de novo designed Coiled Coil CC-Tri-N13 -

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Basic information

Entry
Database: PDB / ID: 4dzk
TitleA de novo designed Coiled Coil CC-Tri-N13
ComponentsCOILED-COIL PEPTIDE CC-TRI-N13
KeywordsDE NOVO PROTEIN
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 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: 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
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: COILED-COIL PEPTIDE CC-TRI-N13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,4672
Polymers3,4321
Non-polymers351
Water25214
1
A: COILED-COIL PEPTIDE CC-TRI-N13
hetero molecules

A: COILED-COIL PEPTIDE CC-TRI-N13
hetero molecules

A: COILED-COIL PEPTIDE CC-TRI-N13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4026
Polymers10,2963
Non-polymers1063
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area3500 Å2
ΔGint-46 kcal/mol
Surface area5630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.150, 38.150, 44.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-101-

CL

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Components

#1: Protein/peptide COILED-COIL PEPTIDE CC-TRI-N13


Mass: 3431.996 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Solid state peptide synthesis / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.71 Å3/Da / Density % sol: 54.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 2.0 M (NH4)2SO4, 5 % v/v 2-propanol, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.571
11-h,-k,l20.429
ReflectionResolution: 1.79→44.3 Å / Num. obs: 3777 / % possible obs: 99.7 % / Observed criterion σ(I): 7.1
Reflection shellResolution: 1.8→1.9 Å / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→44.3 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.901 / SU B: 3.013 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.026 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26899 168 4.5 %RANDOM
Rwork0.23019 ---
obs0.23174 3607 99.37 %-
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: 21.455 Å2
Baniso -1Baniso -2Baniso -3
1-12.46 Å20 Å20 Å2
2--12.46 Å20 Å2
3----24.92 Å2
Refinement stepCycle: LAST / Resolution: 1.79→44.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms221 0 1 14 236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.023223
X-RAY DIFFRACTIONr_bond_other_d0.0010.02153
X-RAY DIFFRACTIONr_angle_refined_deg1.0331.942297
X-RAY DIFFRACTIONr_angle_other_deg2.8563385
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.932528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.02428.758
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.9481549
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0430.235
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.02234
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0233
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_it2.6378143
X-RAY DIFFRACTIONr_mcbond_other0.756858
X-RAY DIFFRACTIONr_mcangle_it3.98212225
X-RAY DIFFRACTIONr_scbond_it7.4371680
X-RAY DIFFRACTIONr_scangle_it11.5352472
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.786→1.832 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 13 -
Rwork0.156 261 -
obs--98.21 %

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