[English] 日本語
Yorodumi
- PDB-6q5k: Crystal structure of a CC-Hex mutant that forms an antiparallel f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6q5k
TitleCrystal structure of a CC-Hex mutant that forms an antiparallel four-helix coiled coil CC-Hex*-L24K
ComponentsCC-Hex*-L24K
KeywordsDE NOVO PROTEIN / coiled coil / tetramer / synthetic / antiparallel / cc-hex
Function / homologyAMMONIUM ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsWood, C.W. / Beesley, J.L. / Rhys, G.G. / Brady, R.L. / Woolfson, D.N.
Funding support United Kingdom, Belgium, 5items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J014400/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/G036764/1 United Kingdom
European Research Council340764 Belgium
Biotechnology and Biological Sciences Research CouncilBB/R00661X/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/K03927X/1 United Kingdom
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Navigating the Structural Landscape of De Novo alpha-Helical Bundles.
Authors: Rhys, G.G. / Wood, C.W. / Beesley, J.L. / Zaccai, N.R. / Burton, A.J. / Brady, R.L. / Thomson, A.R. / Woolfson, D.N.
History
DepositionDec 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CC-Hex*-L24K
B: CC-Hex*-L24K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7266
Polymers6,5022
Non-polymers2244
Water57632
1
A: CC-Hex*-L24K
B: CC-Hex*-L24K
hetero molecules

A: CC-Hex*-L24K
B: CC-Hex*-L24K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,45212
Polymers13,0044
Non-polymers4488
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area5880 Å2
ΔGint-71 kcal/mol
Surface area6590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.280, 69.280, 35.441
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-101-

NH4

-
Components

#1: Protein/peptide CC-Hex*-L24K


Mass: 3250.893 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4N
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 34.86 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.05 M Tris, 0.75 M ammonium sulfate

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.65→24.78 Å / Num. obs: 6134 / % possible obs: 96.5 % / Redundancy: 20.4 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.018 / Rrim(I) all: 0.073 / Net I/σ(I): 17.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.65-1.6818.81.3562.72690.6820.3161.393100
9.04-24.7814.50.02950.45310.0080.0395.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
MOSFLMdata reduction
Aimless0.7.1data scaling
PHASER7.0.06phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→24.78 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.649 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.106 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21834 313 5.1 %RANDOM
Rwork0.17174 ---
obs0.17395 5821 95.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.017 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20.2 Å20 Å2
2--0.4 Å20 Å2
3----1.28 Å2
Refinement stepCycle: 1 / Resolution: 1.65→24.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms400 0 13 32 445
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.013441
X-RAY DIFFRACTIONr_bond_other_d0.0020.017474
X-RAY DIFFRACTIONr_angle_refined_deg1.8561.639588
X-RAY DIFFRACTIONr_angle_other_deg1.5181.5931107
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.409555
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.14525.62516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.3915100
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0950.259
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02467
X-RAY DIFFRACTIONr_gen_planes_other0.0030.0269
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0712.184221
X-RAY DIFFRACTIONr_mcbond_other2.0642.162220
X-RAY DIFFRACTIONr_mcangle_it3.3843.192277
X-RAY DIFFRACTIONr_mcangle_other3.3833.217278
X-RAY DIFFRACTIONr_scbond_it2.4542.687220
X-RAY DIFFRACTIONr_scbond_other2.452.695221
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.733.855312
X-RAY DIFFRACTIONr_long_range_B_refined6.41726.041520
X-RAY DIFFRACTIONr_long_range_B_other6.41126.119521
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 22 -
Rwork0.29 390 -
obs--89.76 %
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)
12.61232.42082.00523.22551.81333.011-0.26680.19760.0399-0.07010.0548-0.052-0.06160.40050.21190.1172-0.01020.00360.12450.03160.0489-8.922-31.454-6.476
20.99462.3205-0.55047.0907-0.81430.6093-0.09070.1110.0288-0.00040.05120.0955-0.0091-0.14870.03950.1147-0.0138-0.03140.0633-0.0040.0157-18.168-23.7740.457
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 24
2X-RAY DIFFRACTION2B1 - 27

+
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