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- PDB-5ez8: A de novo designed heptameric coiled coil CC-Hept-I-C-I -

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Basic information

Entry
Database: PDB / ID: 5ez8
TitleA de novo designed heptameric coiled coil CC-Hept-I-C-I
ComponentsCC-Hept-I-C-I
KeywordsDE NOVO PROTEIN / Coiled coil / heptamer / de novo assembly
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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-I-C-I
B: CC-Hept-I-C-I
C: CC-Hept-I-C-I
D: CC-Hept-I-C-I
E: CC-Hept-I-C-I
F: CC-Hept-I-C-I
G: CC-Hept-I-C-I


Theoretical massNumber of molelcules
Total (without water)22,5887
Polymers22,5887
Non-polymers00
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11890 Å2
ΔGint-114 kcal/mol
Surface area9990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.340, 47.850, 129.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein/peptide
CC-Hept-I-C-I


Mass: 3226.848 Da / Num. of mol.: 7 / Mutation: L22C / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.62 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2 M NaCl, 0.1 M Na cacodylate at pH 6.0 with 8% w/v PEG 8,000.

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.969 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 1.95→43.07 Å / Num. obs: 17242 / % possible obs: 96.3 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 5.2
Reflection shellResolution: 1.95→2 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 1.8 / % possible all: 98.2

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Processing

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

4pna


Resolution: 1.95→43.07 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2431 871 5.11 %
Rwork0.2039 --
obs0.2059 17242 96.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→43.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1570 0 0 84 1654
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081584
X-RAY DIFFRACTIONf_angle_d0.8752111
X-RAY DIFFRACTIONf_dihedral_angle_d12.852601
X-RAY DIFFRACTIONf_chiral_restr0.043246
X-RAY DIFFRACTIONf_plane_restr0.004252
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.07220.26171660.25042685X-RAY DIFFRACTION97
2.0722-2.23220.25741350.20172667X-RAY DIFFRACTION95
2.2322-2.45680.24591550.23232630X-RAY DIFFRACTION94
2.4568-2.81220.26111600.20872692X-RAY DIFFRACTION95
2.8122-3.54270.25011270.19622707X-RAY DIFFRACTION94
3.5427-38.45820.21721280.18972788X-RAY DIFFRACTION91
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)
11.78950.63542.31211.40161.21543.4945-0.0879-0.05630.18010.0792-0.04620.0079-1.1919-0.00890.14910.2871-0.0150.03270.1461-0.04030.278789.331510.7751280.9837
21.37670.0304-0.55510.9522-0.82754.7861-0.1051-0.0354-0.00910.2216-0.06690.33880.8566-0.89330.07010.2619-0.10840.09710.2267-0.01010.294979.424-6.2914281.5033
31.59820.23830.33281.5838-0.24342.3801-0.0512-0.09350.11710.1744-0.0979-0.1202-0.18481.16150.27630.1917-0.0171-0.00250.2487-0.00970.235595.71994.6629281.1086
42.036-0.30261.03732.7803-1.29372.13950.1823-0.1305-0.06280.37830.1181-0.04170.10890.6252-0.18410.20650.0352-0.00510.15570.02240.211895.1322-3.8769281.7016
51.4578-0.0435-1.42811.5037-0.30872.0876-0.2306-0.2642-0.24450.4574-0.03890.04051.19710.21590.33570.3560.01130.04990.17090.06290.266587.7576-8.815281.7953
61.5253-0.27120.31141.3760.89187.0859-0.1429-0.11610.33090.0423-0.20480.1407-0.6492-0.80970.36010.2350.0720.04240.1856-0.0330.288180.47229.4071280.2789
71.39390.06010.38511.41341.78292.91340.0162-0.0194-0.02520.1979-0.23130.27480.0644-1.46450.28480.1804-0.01510.09910.2911-0.02230.296476.38541.933281.388
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 31 )
2X-RAY DIFFRACTION2chain 'B' and (resid 2 through 30 )
3X-RAY DIFFRACTION3chain 'C' and (resid 2 through 31 )
4X-RAY DIFFRACTION4chain 'D' and (resid 2 through 31 )
5X-RAY DIFFRACTION5chain 'E' and (resid 2 through 31 )
6X-RAY DIFFRACTION6chain 'F' and (resid 2 through 30 )
7X-RAY DIFFRACTION7chain 'G' and (resid 2 through 31 )

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