[English] 日本語
Yorodumi
- PDB-8bcs: X-ray crystal structure of a de novo designed helix-loop-helix ho... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8bcs
TitleX-ray crystal structure of a de novo designed helix-loop-helix homodimer in an anti arrangement, CC-HP1.0
ComponentsCC-HP1.0
KeywordsDE NOVO PROTEIN / coiled coil / 4-helix bundle / de novo protein design / helix-loop-helix dimer
Function / homologyACETATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsEdgell, C.L. / Mylemans, B. / Naudin, E.A. / Smith, A.J. / Savery, N.J. / Woolfson, D.N.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S002820/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V006231/1 United Kingdom
Max Planck Bristol Centre for Minimal Biology - University of Bristol United Kingdom
CitationJournal: Acs Synth Biol / Year: 2023
Title: Design and Selection of Heterodimerizing Helical Hairpins for Synthetic Biology.
Authors: Smith, A.J. / Naudin, E.A. / Edgell, C.L. / Baker, E.G. / Mylemans, B. / FitzPatrick, L. / Herman, A. / Rice, H.M. / Andrews, D.M. / Tigue, N. / Woolfson, D.N. / Savery, N.J.
History
DepositionOct 17, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CC-HP1.0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,3342
Polymers5,2751
Non-polymers591
Water00
1
A: CC-HP1.0
hetero molecules

A: CC-HP1.0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6694
Polymers10,5512
Non-polymers1182
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area2290 Å2
ΔGint-28 kcal/mol
Surface area5340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.438, 36.438, 59.329
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

-
Components

#1: Protein CC-HP1.0


Mass: 5275.271 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 42.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M sodium acetate trihydrate, 0.1 M sodium cacodylate, 30% w/v PEG 8000, pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.99→31.56 Å / Num. obs: 3400 / % possible obs: 100 % / Redundancy: 16.5 % / Biso Wilson estimate: 53.42 Å2 / CC1/2: 1 / Rrim(I) all: 0.038 / Net I/σ(I): 27
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.99-2.028.71.11610.61.81397.6
5.39-31.5670.920410.024

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Q5S

6q5s


Resolution: 2.1→31.56 Å / SU ML: 0.2354 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.8234
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2645 152 5.25 %
Rwork0.2375 2743 -
obs0.2396 2895 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.81 Å2
Refinement stepCycle: LAST / Resolution: 2.1→31.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms326 0 4 0 330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008331
X-RAY DIFFRACTIONf_angle_d0.9875449
X-RAY DIFFRACTIONf_chiral_restr0.04659
X-RAY DIFFRACTIONf_plane_restr0.004456
X-RAY DIFFRACTIONf_dihedral_angle_d19.5999108
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.260.3856280.3346531X-RAY DIFFRACTION99.82
2.26-2.490.4511210.3389549X-RAY DIFFRACTION100
2.49-2.850.4161390.3457520X-RAY DIFFRACTION100
2.85-3.590.3544300.2663550X-RAY DIFFRACTION100
3.59-31.560.18340.1943593X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -3.23793364477 Å / Origin y: -7.9972962818 Å / Origin z: 4.18976254378 Å
111213212223313233
T0.483465133024 Å2-0.0374709756727 Å20.033723910567 Å2-0.619154983932 Å20.0079117833747 Å2--0.391603565579 Å2
L7.76725937758 °2-1.61007906951 °2-2.6977934456 °2-8.10963136919 °22.20682987521 °2--5.50614022277 °2
S-0.0923535218427 Å °-1.09556059213 Å °-0.273632042493 Å °0.401727018083 Å °0.549688727755 Å °0.514127401144 Å °-0.335092846466 Å °1.17658978658 Å °-0.4838582918 Å °
Refinement TLS groupSelection details: chain 'A' and (resid 1 through 49 )

+
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://pdbjlvh1.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