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- PDB-5ez9: A de novo designed heptameric coiled coil CC-Hept-I-H-I -

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Basic information

Entry
Database: PDB / ID: 5ez9
TitleA de novo designed heptameric coiled coil CC-Hept-I-H-I
ComponentsCC-Hept-L22H
KeywordsDE NOVO PROTEIN / Coiled coil / heptamer / de novo design
Function / homologyHEXANE-1,6-DIOL
Function and homology information
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
Revision 1.3Nov 20, 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-L22H
B: CC-Hept-L22H
C: CC-Hept-L22H
D: CC-Hept-L22H
E: CC-Hept-L22H
F: CC-Hept-L22H
G: CC-Hept-L22H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7508
Polymers23,6327
Non-polymers1181
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12090 Å2
ΔGint-111 kcal/mol
Surface area10260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.400, 63.030, 70.122
Angle α, β, γ (deg.)90.00, 108.40, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein/peptide
CC-Hept-L22H


Mass: 3376.010 Da / Num. of mol.: 7 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.77 Å3/Da / Density % sol: 55.7 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M MgSO4, 0.1 M Tris at ph 8.5 with 3.4 M 1,6-hexanediol

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→43.15 Å / Num. obs: 23051 / % possible obs: 96.3 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 5.1
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 2.7 / % possible all: 95.4

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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: 1.8→43.15 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2166 1180 5.12 %
Rwork0.1749 --
obs0.177 23031 95.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→43.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1616 0 8 152 1776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081644
X-RAY DIFFRACTIONf_angle_d0.8492190
X-RAY DIFFRACTIONf_dihedral_angle_d12.317631
X-RAY DIFFRACTIONf_chiral_restr0.047246
X-RAY DIFFRACTIONf_plane_restr0.003265
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.88190.24231190.20392719X-RAY DIFFRACTION95
1.8819-1.98120.25731460.19332674X-RAY DIFFRACTION95
1.9812-2.10530.21131510.18342691X-RAY DIFFRACTION95
2.1053-2.26780.19381670.14852718X-RAY DIFFRACTION96
2.2678-2.4960.1931370.15892753X-RAY DIFFRACTION96
2.496-2.85710.22961430.16932741X-RAY DIFFRACTION97
2.8571-3.59940.20951660.17132760X-RAY DIFFRACTION97
3.5994-43.16730.22371510.18682795X-RAY DIFFRACTION96
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)
17.6431-3.0128-5.84592.42122.71626.95030.01850.33110.2824-0.0526-0.0323-0.0537-0.0274-0.372-0.09950.10390.0012-0.05050.07750.01280.087749.248957.502571.7943
27.00311.9698-4.66063.0677-1.46234.0892-0.0855-0.1776-0.046-0.01040.07370.05090.0655-0.0130.04580.12640.0051-0.03340.05690.0140.063952.92339.703580.3968
36.8348-1.5036-6.09572.77351.74027.09480.0626-0.05610.2240.07270.05230.0514-0.01220.0328-0.20560.0916-0.0017-0.03640.0476-0.0180.091253.399759.945279.5543
48.57121.0606-6.34052.4041-0.44296.53080.1372-0.51020.44060.2722-0.01420.1699-0.00760.3161-0.16690.1580.0055-0.04360.1083-0.04010.111356.71354.359786.2643
58.08581.6437-6.75231.6871-1.49356.7365-0.0434-0.5381-0.10240.1154-0.1015-0.05550.07540.36860.12780.14980.0046-0.0450.08340.01130.072757.334945.640786.1632
65.3671-0.2984-3.86490.92170.84225.3316-0.0490.2868-0.0250.0278-0.04420.04050.0687-0.22820.09720.1083-0.0097-0.04120.0780.00370.063746.751149.472969.322
78.1764-0.6178-5.58512.2390.5084.8122-0.32650.0764-0.4898-0.01880.12170.12930.2689-0.08310.15720.1365-0.0197-0.02710.05530.00990.083449.210641.441272.7133
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 30 )

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