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- PDB-5f2y: A de novo designed heptameric coiled coil CC-Hept-homoCys-H-E -

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Basic information

Entry
Database: PDB / ID: 5f2y
TitleA de novo designed heptameric coiled coil CC-Hept-homoCys-H-E
ComponentsCC-Hept-hCys-H-E
KeywordsDE NOVO PROTEIN / Coiled coil / heptamer / de novo design
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBurton, A.J. / Brady, R.L. / Woolfson, D.N.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research Council340764 United Kingdom
CitationJournal: Nat.Chem. / Year: 2016
Title: Installing hydrolytic activity into a completely de novo protein framework.
Authors: Burton, A.J. / Thomson, A.R. / Dawson, W.M. / Brady, R.L. / Woolfson, D.N.
History
DepositionDec 2, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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 1.3Mar 6, 2024Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CC-Hept-hCys-H-E
B: CC-Hept-hCys-H-E
C: CC-Hept-hCys-H-E
D: CC-Hept-hCys-H-E
E: CC-Hept-hCys-H-E
F: CC-Hept-hCys-H-E
G: CC-Hept-hCys-H-E


Theoretical massNumber of molelcules
Total (without water)23,7727
Polymers23,7727
Non-polymers00
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9940 Å2
ΔGint-91 kcal/mol
Surface area9170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.250, 61.980, 68.710
Angle α, β, γ (deg.)90.00, 110.92, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein/peptide
CC-Hept-hCys-H-E


Mass: 3395.978 Da / Num. of mol.: 7 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M HEPES at pH 7.0 with 18% w/v PEG 12000.

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.1→32.09 Å / Num. obs: 14347 / % possible obs: 99.9 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 6.4
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 2.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4pna

4pna


Resolution: 2.1→32.09 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2683 706 4.95 %random selection
Rwork0.2208 ---
obs0.2232 14264 99.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→32.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1350 0 0 85 1435
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071386
X-RAY DIFFRACTIONf_angle_d0.9131857
X-RAY DIFFRACTIONf_dihedral_angle_d14.571506
X-RAY DIFFRACTIONf_chiral_restr0.041203
X-RAY DIFFRACTIONf_plane_restr0.003238
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.26220.30281350.25012692X-RAY DIFFRACTION100
2.2622-2.48980.29351440.23142715X-RAY DIFFRACTION100
2.4898-2.84990.26491380.21752713X-RAY DIFFRACTION99
2.8499-3.58980.27551430.22972689X-RAY DIFFRACTION100
3.5898-32.09340.25261460.20862749X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1918-0.01550.15470.25460.00840.18660.18930.030.8845-0.0074-0.0647-0.2205-0.34340.1078-0.00110.3242-0.02350.07450.32080.09330.523-62.07752.019925.6608
20.4196-0.04930.32310.43880.09490.25930.0850.2783-1.0599-0.1865-0.0613-0.22470.12910.14610.00050.28370.0476-0.00450.2723-0.00350.354-60.0891-17.092828.7051
30.30650.01640.28190.622-0.33620.49680.17740.34970.5719-0.17250.0043-0.098-0.30920.2321-0.00070.30420.0190.05130.36850.13480.3388-66.4132-1.542718.5416
40.17020.06090.30580.07770.06310.56460.14931.6202-0.0561-0.2414-0.27050.0315-0.0468-0.5080.00240.37820.03470.02320.4902-0.02120.2965-67.5579-9.647716.6378
50.08770.00940.15110.27850.01710.24150.03340.8605-0.8705-0.6423-0.17770.22610.1774-0.14130.00120.3859-0.01380.03980.3209-0.11030.4178-64.9426-16.695121.0055
60.34660.02680.39680.24680.01580.46440.2951-0.51280.12160.0788-0.3389-0.2665-0.57750.3969-0.00090.2692-0.00840.0450.3093-0.00310.4297-58.3768-2.217832.1716
70.3165-0.04470.35390.2073-0.06510.42570.1174-0.3537-0.42060.1334-0.0392-0.03820.28140.50610.00050.28830.0049-0.03320.3226-0.01840.3458-57.6917-10.888533.6982
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 18 )
2X-RAY DIFFRACTION2chain 'B' and (resid 2 through 18 )
3X-RAY DIFFRACTION3chain 'C' and (resid 2 through 18 )
4X-RAY DIFFRACTION4chain 'D' and (resid 2 through 18 )
5X-RAY DIFFRACTION5chain 'E' and (resid 2 through 18 )
6X-RAY DIFFRACTION6chain 'F' and (resid 2 through 18 )
7X-RAY DIFFRACTION7chain 'G' and (resid 2 through 18 )

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