[English] 日本語
Yorodumi
- PDB-6jc6: Crystal structure of the purple chromoprotein of Stichodactyla ha... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6jc6
TitleCrystal structure of the purple chromoprotein of Stichodactyla haddoni with a Glu-Tyr-Gly tri-peptide chromophore
ComponentsshCP
KeywordsFLUORESCENT PROTEIN / Sea anemone / Green fluorescent protein / UV absorption / emission spectra / biomarker
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / Beta Barrel / Mainly Beta / shCP
Function and homology information
Biological speciesStichodactyla haddoni (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKo, T.P. / Huang, K.F. / Chang, H.Y.
Funding support Taiwan, 3items
OrganizationGrant numberCountry
Academia Sinica (Taiwan)104-2311-B-110-002-MY2 Taiwan
Academia Sinica (Taiwan)AS-KPQ-105-TPP Taiwan
Academia Sinica (Taiwan)107-0210-01-19-04 Taiwan
CitationJournal: Int. J. Biol. Macromol. / Year: 2019
Title: Crystal structure of the blue fluorescent protein with a Leu-Leu-Gly tri-peptide chromophore derived from the purple chromoprotein of Stichodactyla haddoni.
Authors: Chang, H.Y. / Ko, T.P. / Chang, Y.C. / Huang, K.F. / Lin, C.Y. / Chou, H.Y. / Chiang, C.Y. / Tsai, H.J.
History
DepositionJan 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Nov 22, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: shCP
B: shCP
C: shCP
D: shCP
E: shCP
F: shCP
G: shCP
H: shCP


Theoretical massNumber of molelcules
Total (without water)209,1668
Polymers209,1668
Non-polymers00
Water32,4091799
1
A: shCP
C: shCP


Theoretical massNumber of molelcules
Total (without water)52,2922
Polymers52,2922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-14 kcal/mol
Surface area17950 Å2
MethodPISA
2
B: shCP
D: shCP


Theoretical massNumber of molelcules
Total (without water)52,2922
Polymers52,2922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-11 kcal/mol
Surface area17760 Å2
MethodPISA
3
E: shCP
G: shCP


Theoretical massNumber of molelcules
Total (without water)52,2922
Polymers52,2922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-12 kcal/mol
Surface area18000 Å2
MethodPISA
4
F: shCP
H: shCP


Theoretical massNumber of molelcules
Total (without water)52,2922
Polymers52,2922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-14 kcal/mol
Surface area17780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.882, 98.330, 197.891
Angle α, β, γ (deg.)90.00, 100.37, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-652-

HOH

21D-585-

HOH

31F-459-

HOH

-
Components

#1: Protein
shCP


Mass: 26145.812 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stichodactyla haddoni (sea anemone) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4V8H023*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1799 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M lithium acetate and 20% PEG 3350

-
Data collection

DiffractionMean temperature: 123 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→29.9 Å / Num. obs: 143275 / % possible obs: 99.7 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 26.4
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.671 / Num. unique obs: 14815

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YZW

1yzw


Resolution: 1.9→27.936 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.99
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I_MINUS AND I_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2198 2038 1.42 %
Rwork0.1887 --
obs0.1891 143275 93.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→27.936 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14122 0 0 1806 15928
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00414828
X-RAY DIFFRACTIONf_angle_d0.80920051
X-RAY DIFFRACTIONf_dihedral_angle_d14.6528861
X-RAY DIFFRACTIONf_chiral_restr0.0522082
X-RAY DIFFRACTIONf_plane_restr0.0042597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8999-1.94410.3039610.26794081X-RAY DIFFRACTION41
1.9441-1.99270.2784980.25667634X-RAY DIFFRACTION76
1.9927-2.04650.26791500.23929365X-RAY DIFFRACTION94
2.0465-2.10670.26771370.23489805X-RAY DIFFRACTION98
2.1067-2.17470.28071380.23329953X-RAY DIFFRACTION100
2.1747-2.25240.27921390.2319974X-RAY DIFFRACTION100
2.2524-2.34250.25921420.216910042X-RAY DIFFRACTION100
2.3425-2.44910.24721500.210410041X-RAY DIFFRACTION100
2.4491-2.57810.25161400.21269957X-RAY DIFFRACTION100
2.5781-2.73950.23291430.198410054X-RAY DIFFRACTION100
2.7395-2.95080.22891400.199110004X-RAY DIFFRACTION100
2.9508-3.24740.19651530.186710025X-RAY DIFFRACTION100
3.2474-3.71640.20311380.158710024X-RAY DIFFRACTION100
3.7164-4.67870.16271520.140410111X-RAY DIFFRACTION100
4.6787-27.93950.18921570.157410167X-RAY DIFFRACTION100

+
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