[English] 日本語
Yorodumi
- PDB-4h8o: Crystal structure of a parallel 6-helix coiled coil CC-Hex-N24 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4h8o
TitleCrystal structure of a parallel 6-helix coiled coil CC-Hex-N24
ComponentsCC-Hex-N24
KeywordsDE NOVO PROTEIN / CC-Hex / parallel / hexameric coiled coil / N-terminal acetylation / C-terminal amidation
Biological speciesSynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.598 Å
AuthorsChi, B. / Zaccai, N.R. / Brady, R.L. / Woolfson, D.N.
CitationJournal: To be Published
Title: TBA
Authors: Chi, B. / Zaccai, N.R. / Brady, R.L. / Woolfson, D.N.
History
DepositionSep 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CC-Hex-N24
B: CC-Hex-N24
C: CC-Hex-N24
D: CC-Hex-N24
E: CC-Hex-N24
F: CC-Hex-N24


Theoretical massNumber of molelcules
Total (without water)19,2776
Polymers19,2776
Non-polymers00
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9610 Å2
ΔGint-90 kcal/mol
Surface area10150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.880, 111.050, 35.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-123-

HOH

21B-125-

HOH

-
Components

#1: Protein/peptide
CC-Hex-N24


Mass: 3212.780 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: standard F-moc solid phase peptide synthesis / Source: (synth.) Synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 3% D-sorbitol, 20 mM sodium formate, 20 mM ammonium acetate, 20 mM trisodium citrate, 20 mM sodium potassium L-tartrate, 20 mM sodium oxamate; 100 mM MES/imidazole pH 6.5; and 10 % PEG 20K, ...Details: 3% D-sorbitol, 20 mM sodium formate, 20 mM ammonium acetate, 20 mM trisodium citrate, 20 mM sodium potassium L-tartrate, 20 mM sodium oxamate; 100 mM MES/imidazole pH 6.5; and 10 % PEG 20K, 20 % PEG MME 550, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.598→50.9 Å / Num. all: 27793 / Num. obs: 27487

-
Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.7_650) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3R46

3r46


Resolution: 1.598→46.256 Å / SU ML: 0.26 / σ(F): 1.04 / Phase error: 32.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2493 2501 4.99 %
Rwork0.2147 --
obs0.2164 50075 95.95 %
all-50632 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.059 Å2 / ksol: 0.372 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.7934 Å20 Å20 Å2
2--1.0109 Å2-0 Å2
3---0.7824 Å2
Refinement stepCycle: LAST / Resolution: 1.598→46.256 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1362 0 0 219 1581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161363
X-RAY DIFFRACTIONf_angle_d1.4651812
X-RAY DIFFRACTIONf_dihedral_angle_d14.56522
X-RAY DIFFRACTIONf_chiral_restr0.094210
X-RAY DIFFRACTIONf_plane_restr0.005234
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.598-1.62870.51821190.44692345X-RAY DIFFRACTION84
1.6287-1.66190.47641070.43342470X-RAY DIFFRACTION91
1.6619-1.69810.43671370.41422611X-RAY DIFFRACTION92
1.6981-1.73760.35851360.37972560X-RAY DIFFRACTION94
1.7376-1.7810.35661380.36432585X-RAY DIFFRACTION94
1.781-1.82920.40191380.33982602X-RAY DIFFRACTION94
1.8292-1.8830.38821320.3292580X-RAY DIFFRACTION93
1.883-1.94380.30811390.30542648X-RAY DIFFRACTION97
1.9438-2.01330.30721310.24282669X-RAY DIFFRACTION96
2.0133-2.09390.27671720.21692681X-RAY DIFFRACTION98
2.0939-2.18920.25571390.21392620X-RAY DIFFRACTION97
2.1892-2.30460.25821320.18352740X-RAY DIFFRACTION98
2.3046-2.4490.19571610.16822732X-RAY DIFFRACTION99
2.449-2.6380.22011280.15722755X-RAY DIFFRACTION100
2.638-2.90350.24991500.18482743X-RAY DIFFRACTION100
2.9035-3.32350.21691520.17452732X-RAY DIFFRACTION100
3.3235-4.18690.16811560.15822764X-RAY DIFFRACTION100
4.1869-46.27540.23261340.20812737X-RAY DIFFRACTION99

+
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