[English] 日本語
Yorodumi
- PDB-7nfi: An octameric barrel state of a de novo coiled-coil assembly: CC-T... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7nfi
TitleAn octameric barrel state of a de novo coiled-coil assembly: CC-Type2-(LaId)4-L7Y.
ComponentsCC-Type2-(LaId)4-L7Y
KeywordsDE NOVO PROTEIN / Coiled coil / synthetic peptide / homomeric assembly
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsRhys, G.G. / Dawson, W.M. / Brady, R.L. / Woolfson, D.N.
Funding supportEuropean Union, United Kingdom, 2items
OrganizationGrant numberCountry
European Research Council (ERC)340764European Union
Engineering and Physical Sciences Research CouncilEP/G036764/1 United Kingdom
CitationJournal: Nat Commun / Year: 2023
Title: Differential sensing with arrays of de novo designed peptide assemblies.
Authors: Dawson, W.M. / Shelley, K.L. / Fletcher, J.M. / Scott, D.A. / Lombardi, L. / Rhys, G.G. / LaGambina, T.J. / Obst, U. / Burton, A.J. / Cross, J.A. / Davies, G. / Martin, F.J.O. / Wiseman, F.J. ...Authors: Dawson, W.M. / Shelley, K.L. / Fletcher, J.M. / Scott, D.A. / Lombardi, L. / Rhys, G.G. / LaGambina, T.J. / Obst, U. / Burton, A.J. / Cross, J.A. / Davies, G. / Martin, F.J.O. / Wiseman, F.J. / Brady, R.L. / Tew, D. / Wood, C.W. / Woolfson, D.N.
History
DepositionFeb 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Data collection / Database references / Category: citation / citation_author / diffrn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn.ambient_temp
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CC-Type2-(LaId)4-L7Y
B: CC-Type2-(LaId)4-L7Y


Theoretical massNumber of molelcules
Total (without water)6,5702
Polymers6,5702
Non-polymers00
Water84747
1
A: CC-Type2-(LaId)4-L7Y
B: CC-Type2-(LaId)4-L7Y

A: CC-Type2-(LaId)4-L7Y
B: CC-Type2-(LaId)4-L7Y

A: CC-Type2-(LaId)4-L7Y
B: CC-Type2-(LaId)4-L7Y

A: CC-Type2-(LaId)4-L7Y
B: CC-Type2-(LaId)4-L7Y


Theoretical massNumber of molelcules
Total (without water)26,2798
Polymers26,2798
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area13810 Å2
ΔGint-128 kcal/mol
Surface area11770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.393, 47.393, 127.164
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-122-

HOH

21A-124-

HOH

31B-118-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 1 - 30 / Label seq-ID: 2 - 31

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein/peptide CC-Type2-(LaId)4-L7Y


Mass: 3284.887 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.73 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: After 1:1 dilution with the peptide solution, the resulting conditions were 100 mM ammonium formate and 10% w/v PEG 3350.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.42→44.41 Å / Num. obs: 14194 / % possible obs: 100 % / Redundancy: 20.6 % / Biso Wilson estimate: 25.45 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.011 / Rrim(I) all: 0.049 / Net I/σ(I): 24.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.42-1.4613.24.9840.810220.4451.4035.183100
6.35-44.41190.02372.720710.0060.02399.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
PDB_EXTRACT3.25data extraction
DIALS1.14.13-g10ecfbb15-releasedata reduction
Aimless0.7.4data scaling
xia20.5.902-gffa11588-dials-1.14data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: model helices

Resolution: 1.42→44.41 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.321 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2178 732 5.2 %RANDOM
Rwork0.175 ---
obs0.1772 13458 99.96 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso max: 120.95 Å2 / Biso mean: 30.615 Å2 / Biso min: 19.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å2-0 Å2
2--0.11 Å2-0 Å2
3----0.22 Å2
Refinement stepCycle: final / Resolution: 1.42→44.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms458 0 6 47 511
Biso mean--41.4 51.2 -
Num. residues----60
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.013502
X-RAY DIFFRACTIONr_bond_other_d0.0020.017519
X-RAY DIFFRACTIONr_angle_refined_deg1.4921.633676
X-RAY DIFFRACTIONr_angle_other_deg1.5161.5851201
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.081564
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.68825.23821
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.43715101
X-RAY DIFFRACTIONr_chiral_restr0.0920.267
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02565
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0299
X-RAY DIFFRACTIONr_rigid_bond_restr3.07531021
Refine LS restraints NCS

Ens-ID: 1 / Number: 858 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.42→1.457 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 51 -
Rwork0.322 971 -
all-1022 -
obs--100 %

+
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