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- PDB-5eze: A de novo designed heptameric coiled coil CC-Hept-I18betaMeCys-L2... -

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Basic information

Entry
Database: PDB / ID: 5eze
TitleA de novo designed heptameric coiled coil CC-Hept-I18betaMeCys-L22H-I25E
ComponentsCC-Hept-bMeCys-His-Glu
KeywordsDE NOVO PROTEIN / Coiled coil / heptamer / de novo structure
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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CC-Hept-bMeCys-His-Glu
B: CC-Hept-bMeCys-His-Glu
C: CC-Hept-bMeCys-His-Glu
D: CC-Hept-bMeCys-His-Glu
E: CC-Hept-bMeCys-His-Glu
F: CC-Hept-bMeCys-His-Glu
G: CC-Hept-bMeCys-His-Glu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9569
Polymers23,7727
Non-polymers1842
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10700 Å2
ΔGint-78 kcal/mol
Surface area9670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.450, 60.490, 68.812
Angle α, β, γ (deg.)90.00, 112.43, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein/peptide
CC-Hept-bMeCys-His-Glu


Mass: 3395.978 Da / Num. of mol.: 7 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.53 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium formate with 20% w/v PEG 3350.

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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: Nov 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.8→43.833 Å / Num. obs: 21962 / % possible obs: 99.6 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 7.1
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.071 / Mean I/σ(I) obs: 2.6 / % possible all: 99.8

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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→43.83 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2407 1111 5.07 %random selection
Rwork0.2063 ---
obs0.208 21896 99.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→43.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1429 0 12 117 1558
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071466
X-RAY DIFFRACTIONf_angle_d0.8611917
X-RAY DIFFRACTIONf_dihedral_angle_d13.48528
X-RAY DIFFRACTIONf_chiral_restr0.04214
X-RAY DIFFRACTIONf_plane_restr0.003229
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8001-1.8820.2921470.26462585X-RAY DIFFRACTION99
1.882-1.98120.26091130.24522601X-RAY DIFFRACTION99
1.9812-2.10540.27381410.23272562X-RAY DIFFRACTION99
2.1054-2.26790.24731400.18862596X-RAY DIFFRACTION99
2.2679-2.49610.21361350.18822613X-RAY DIFFRACTION99
2.4961-2.85730.21641440.20132580X-RAY DIFFRACTION100
2.8573-3.59960.2261310.20362617X-RAY DIFFRACTION99
3.5996-43.830.25371600.20292631X-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)
14.81511.4109-5.43823.6621-1.61753.89060.2476-0.02330.7118-0.3832-0.0182-0.4642-0.12390.2786-0.25420.2347-0.0040.00120.3070.06830.3179-30.42440.1803-43.0381
25.35651.383-5.53142.7259-0.99044.1786-0.5844-0.1754-1.532-0.01160.0715-0.28170.64270.38240.49540.20790.04-0.02240.25840.00620.3078-33.4144-19.3964-35.8188
32.92763.37453.45463.91163.87994.5035-2.04392.02871.57140.15530.0192-3.3047-1.39664.04221.83950.5865-0.2798-0.0841.12240.14011.0045-18.1408-17.3922-41.3501
47.0959-1.9915-5.58585.09982.15864.25130.40721.08040.6828-0.71930.0865-0.4807-0.4681-0.1421-0.51040.3163-0.0080.01340.4730.07240.2231-35.2227-4.1287-49.0583
56.2595-0.9627-2.90366.36561.94448.0970.11.4268-0.1107-0.5234-0.0337-0.27420.0821-0.5451-0.05610.2277-0.0123-0.02510.4105-0.04720.1111-39.7631-12.297-48.7283
69.1334-3.2615-6.83144.18942.06988.0935-0.16040.5343-0.5003-0.15770.0166-0.42180.12640.10970.18540.2342-0.01950.00020.2329-0.10250.2458-32.6744-19.3396-45.5092
78.45741.1727-5.93534.8202-0.84338.25050.2589-0.65120.5691-0.229-0.1171-0.6668-0.45360.9254-0.09610.1786-0.0465-0.04960.31410.0080.3061-27.1628-2.9423-35.1715
87.73042.038-5.75542.6123-1.84668.133-0.0566-0.3854-0.3642-0.0772-0.0881-0.2717-0.03990.7370.13880.15910.0085-0.08010.29670.00070.1931-25.7403-11.7128-33.6953
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 29 )
2X-RAY DIFFRACTION2chain 'B' and (resid 2 through 20 )
3X-RAY DIFFRACTION3chain 'B' and (resid 21 through 24 )
4X-RAY DIFFRACTION4chain 'C' and (resid 2 through 28 )
5X-RAY DIFFRACTION5chain 'D' and (resid 2 through 22 )
6X-RAY DIFFRACTION6chain 'E' and (resid 2 through 28 )
7X-RAY DIFFRACTION7chain 'F' and (resid 2 through 28 )
8X-RAY DIFFRACTION8chain 'G' and (resid 2 through 28 )

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