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- PDB-5ezc: A de novo designed heptameric coiled coil CC-Hept-I18C-L22H-I25E -

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Basic information

Entry
Database: PDB / ID: 5ezc
TitleA de novo designed heptameric coiled coil CC-Hept-I18C-L22H-I25E
ComponentsCC-Hept-C-H-E
KeywordsDE NOVO PROTEIN / Coiled coil / heptamer
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
DepositionNov 26, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)23,6747
Polymers23,6747
Non-polymers00
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11750 Å2
ΔGint-111 kcal/mol
Surface area10020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.252, 60.880, 69.380
Angle α, β, γ (deg.)90.00, 110.89, 90.00
Int Tables number5
Space group name H-MI121

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Components

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


Mass: 3381.951 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.: 162 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.5 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M MgCl2, 0.1 M Tris at pH 7.0 with 10% w/v PEG

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→53.9 Å / Num. obs: 22242 / % possible obs: 98.9 % / Redundancy: 3 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 7.7
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 2.3 / % possible all: 97.8

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Processing

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

4pna


Resolution: 1.8→44.376 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2196 1135 5.11 %
Rwork0.1871 --
obs0.1888 22206 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→44.376 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1610 0 0 162 1772
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071631
X-RAY DIFFRACTIONf_angle_d0.8192173
X-RAY DIFFRACTIONf_dihedral_angle_d16.204623
X-RAY DIFFRACTIONf_chiral_restr0.035233
X-RAY DIFFRACTIONf_plane_restr0.003273
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8001-1.8820.33811440.28392607X-RAY DIFFRACTION98
1.882-1.98120.28551310.23392608X-RAY DIFFRACTION98
1.9812-2.10540.2791360.21942624X-RAY DIFFRACTION98
2.1054-2.26790.2271310.17432634X-RAY DIFFRACTION99
2.2679-2.49610.24051270.17372644X-RAY DIFFRACTION98
2.4961-2.85730.20041720.17672603X-RAY DIFFRACTION99
2.8573-3.59960.17951440.17512661X-RAY DIFFRACTION99
3.5996-44.38920.21551500.18182690X-RAY DIFFRACTION98
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)
15.58971.6901-6.49071.8923-2.24518.09140.0951-0.09640.4577-0.3821-0.046-0.42350.09250.3305-0.08920.2490.0170.02720.18440.06860.3274-31.2092-1.3391-44.6891
24.53042.4522-5.22673.4104-1.73626.6531-0.47-0.3394-1.2609-0.1880.0043-0.62350.29920.71990.41950.2430.0508-0.03750.2507-0.00690.2992-26.8863-19.2643-38.8053
34.9433-1.9648-4.39634.7761.39825.80310.48311.12870.62-0.7528-0.1657-0.718-0.195-0.3174-0.28880.32340.03380.01240.38270.07820.2399-34.4442-6.4281-51.3912
47.5954-1.3689-5.25444.95331.02216.58-0.17151.2077-0.319-0.5808-0.0281-0.4080.1969-0.34360.11010.3255-0.0316-0.0390.3074-0.06270.1866-35.2351-14.9067-51.5895
55.2589-2.5494-5.61773.25222.10625.5943-0.21490.4345-0.1658-0.20170.2055-0.48990.03720.0284-0.04930.2386-0.0210.00990.1739-0.0930.2699-32.033-20.7853-46.0256
65.2090.369-6.68242.4415-1.83548.75490.3246-0.60180.7936-0.1598-0.1138-0.3602-0.25290.863-0.18350.2098-0.0448-0.03260.27320.00470.2832-27.0684-4.0175-37.654
72.66340.1374-3.8121.5311-0.49427.2783-0.0679-0.2841-0.2208-0.1213-0.0339-0.14880.02620.61550.03310.18260.0023-0.08560.25290.01990.1653-25.1664-11.8973-35.1252
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 30 )
2X-RAY DIFFRACTION2chain 'B' and (resid 2 through 31 )
3X-RAY DIFFRACTION3chain 'C' and (resid 2 through 30 )
4X-RAY DIFFRACTION4chain 'D' and (resid 2 through 30 )
5X-RAY DIFFRACTION5chain 'E' and (resid 2 through 30 )
6X-RAY DIFFRACTION6chain 'F' and (resid 2 through 31 )
7X-RAY DIFFRACTION7chain 'G' and (resid 2 through 31 )

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