[English] 日本語
Yorodumi
- PDB-5f2y: A de novo designed heptameric coiled coil CC-Hept-homoCys-H-E -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
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.

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more