[English] 日本語
Yorodumi
- PDB-4h8f: Crystal structure of a parallel 4-helix coiled coil CC-Hex-II- 22 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4h8f
TitleCrystal structure of a parallel 4-helix coiled coil CC-Hex-II- 22
ComponentsCC-Hex-II-Phi22
KeywordsDE NOVO PROTEIN / CC-Hex related / synthetic coiled coil peptide / N-terminal acetylation / C-terminal amidation
Function / homologyTERTIARY-BUTYL ALCOHOL
Function and homology information
Biological speciesSynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsChi, B. / Zaccai, N.R. / Brady, R.L. / Woolfson, D.N.
CitationJournal: J.Am.Chem.Soc.
Title: TBA
Authors: Chi, B. / Zaccai, N.R. / Brady, R.L. / Woolfson, D.N.
History
DepositionSep 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: pdbx_struct_special_symmetry / software / struct_conn
Item: _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Sep 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CC-Hex-II-Phi22
B: CC-Hex-II-Phi22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2846
Polymers6,9702
Non-polymers3144
Water1,29772
1
A: CC-Hex-II-Phi22
B: CC-Hex-II-Phi22
hetero molecules

A: CC-Hex-II-Phi22
B: CC-Hex-II-Phi22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,56912
Polymers13,9404
Non-polymers6298
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area8960 Å2
ΔGint-27 kcal/mol
Surface area6400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.670, 46.670, 94.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11B-101-

TBU

21B-202-

HOH

31B-228-

HOH

-
Components

#1: Protein/peptide CC-Hex-II-Phi22


Mass: 3484.906 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Standard F-moc peptide synthesis / Source: (synth.) Synthetic construct (others)
#2: Chemical ChemComp-TBU / TERTIARY-BUTYL ALCOHOL / 2-METHYL-2-PROPANOL


Mass: 74.122 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.67 Å3/Da / Density % sol: 66.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25 % tert-butanol and 100 mM Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I2410.97
SYNCHROTRONDiamond I2421.7
Detector
TypeIDDetectorDate
PSI PILATUS 6M1PIXELAug 22, 2011
PSI PILATUS 6M2PIXELAug 22, 2011
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.971
21.71
ReflectionResolution: 1.88→46.7 Å / Num. all: 9046 / Num. obs: 8847

-
Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
PHENIX(phenix.refine: 1.7_650)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3R46

3r46


Resolution: 1.88→46.67 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.924 / SU B: 2.713 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24324 422 4.8 %RANDOM
Rwork0.2072 ---
obs0.20878 8372 97.57 %-
all-8847 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.497 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å20 Å2
2--0.59 Å20 Å2
3----1.19 Å2
Refinement stepCycle: LAST / Resolution: 1.88→46.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms478 0 21 72 571
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022497
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2412.056663
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.061562
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.32228.57114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.5521598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1020.277
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02336
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.7671.5324
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.8112499
X-RAY DIFFRACTIONr_scbond_it5.1273173
X-RAY DIFFRACTIONr_scangle_it8.724.5164
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.88→1.929 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 25 -
Rwork0.396 449 -
obs--74.88 %

+
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