[English] 日本語
Yorodumi
- PDB-2ib6: Structural characterization of a blue chromoprotein and its yello... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ib6
TitleStructural characterization of a blue chromoprotein and its yellow mutant from the sea anemone cnidopus japonicus
ComponentsYellow mutant chromo protein
KeywordsLUMINESCENT PROTEIN / beta barrel / alpha helix / chromoprotein / yellow / chromophore / GFP-like protein
Function / homology
Function and homology information


Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Cj-Blue Y64L
Similarity search - Component
Biological speciesCnidopus japonicus (sea anemone)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChan, M.C.Y. / Bosanac, I. / Ho, D. / Prive, G. / Ikura, M.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structural Characterization of a Blue Chromoprotein and Its Yellow Mutant from the Sea Anemone Cnidopus Japonicus
Authors: Chan, M.C.Y. / Karasawa, S. / Mizuno, H. / Bosanac, I. / Ho, D. / Prive, G.G. / Miyawaki, A. / Ikura, M.
History
DepositionSep 10, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 10, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 25, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_polymer_linkage / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / 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 / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_validate_polymer_linkage.auth_atom_id_1 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Yellow mutant chromo protein
B: Yellow mutant chromo protein
C: Yellow mutant chromo protein
D: Yellow mutant chromo protein
E: Yellow mutant chromo protein
F: Yellow mutant chromo protein
G: Yellow mutant chromo protein
H: Yellow mutant chromo protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,85724
Polymers214,3388
Non-polymers1,52016
Water24,1401340
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13500 Å2
ΔGint-122 kcal/mol
Surface area30500 Å2
MethodPISA
3
A: Yellow mutant chromo protein
B: Yellow mutant chromo protein
C: Yellow mutant chromo protein
D: Yellow mutant chromo protein
F: Yellow mutant chromo protein
G: Yellow mutant chromo protein
H: Yellow mutant chromo protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,06523
Polymers187,5457
Non-polymers1,52016
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13490 Å2
ΔGint-118 kcal/mol
Surface area30630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.079, 126.926, 100.084
Angle α, β, γ (deg.)90.00, 101.97, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a octomer generated from the tetramer in the asymmetric unit.

-
Components

#1: Protein
Yellow mutant chromo protein / cjBlue


Mass: 26792.211 Da / Num. of mol.: 8 / Mutation: Y64L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cnidopus japonicus (sea anemone) / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: A0AQQ8
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1340 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.69 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M NaH2PO4, 20mM Tris-HCl, 150mM NaCl, 20% PEG3350, 20% glycerol, 2mM TCEP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jan 28, 2005 / Details: Helios Multilayer Graded X-ray Optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 121926 / Num. obs: 121926 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 39.65
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 4.1 / Num. unique all: 10246 / % possible all: 88.5

-
Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
CNSrefinement
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IB5

2ib5


Resolution: 2→50 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.244 5761 -random
Rwork0.198 ---
obs0.198 113671 80.3 %-
all-113671 --
Displacement parametersBiso mean: 16.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14352 0 80 1340 15772
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.644
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_improper_angle_d0.68
X-RAY DIFFRACTIONc_mcbond_it1.196
X-RAY DIFFRACTIONc_mcangle_it1.748
X-RAY DIFFRACTIONc_scangle_it3.154
X-RAY DIFFRACTIONc_scbond_it2.294
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.04
RfactorNum. reflection% reflection
Rfree0.29 498 -
Rwork0.25 --
obs--80.3 %

+
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