[English] 日本語
Yorodumi
- PDB-2ote: Crystal structure of a monomeric cyan fluorescent protein in the ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ote
TitleCrystal structure of a monomeric cyan fluorescent protein in the photobleached state
ComponentsGFP-like fluorescent chromoprotein cFP484
KeywordsFLUORESCENT PROTEIN / Beta can
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
Similarity search - Function
Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / GFP-like fluorescent chromoprotein cFP484
Similarity search - Component
Biological speciesClavularia sp. (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsHenderson, J.N. / Ai, H. / Campbell, R.E. / Remington, S.J.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structural basis for reversible photobleaching of a green fluorescent protein homologue.
Authors: Henderson, J.N. / Ai, H.W. / Campbell, R.E. / Remington, S.J.
History
DepositionFeb 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 22, 2012Group: Other
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.5Aug 30, 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 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GFP-like fluorescent chromoprotein cFP484
B: GFP-like fluorescent chromoprotein cFP484
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6573
Polymers49,5982
Non-polymers591
Water8,107450
1
A: GFP-like fluorescent chromoprotein cFP484
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8582
Polymers24,7991
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GFP-like fluorescent chromoprotein cFP484


Theoretical massNumber of molelcules
Total (without water)24,7991
Polymers24,7991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.489, 66.310, 97.203
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer. There are two monomers per asymmetric unit.

-
Components

#1: Protein GFP-like fluorescent chromoprotein cFP484


Mass: 24799.186 Da / Num. of mol.: 2
Mutation: H42N, L44I, S62T, Q66A, L72F, A80P, D81N, R123H, F124L, D125K, M127E, M150L, S162K, S164K, Y173H, C175V, S179T, K182R, V186A, L213V, N216S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clavularia sp. (invertebrata) / Gene: cFP484 / Plasmid: pBAD/HisB / Production host: Escherichia coli (E. coli) / Strain (production host): Top10 / References: UniProt: Q9U6Y3
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 450 / 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: 2.13 Å3/Da / Density % sol: 42.16 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 31% PEG 3400, 0.2 M Lithium Sulfate, 0.1 M Sodium Acetate, 2.9 mM 1-s-Nonyl-beta-D-thioglucoside, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 17, 2006 / Details: Bent conical Si-mirror (Rh coated)
RadiationMonochromator: Bent Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.47→50 Å / Num. obs: 68960 / % possible obs: 94.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.054 / Χ2: 1.075 / Net I/σ(I): 16.4
Reflection shellResolution: 1.47→1.52 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 2.4 / Num. unique all: 6554 / Χ2: 1.081 / % possible all: 91.2

-
Phasing

Phasing MRRfactor: 0.298 / Cor.coef. Fo:Fc: 0.824
Highest resolutionLowest resolution
Translation4 Å15 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
EPMR2.5phasing
SHELXrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
SHELXLrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2OTB with the waters and chromophores removed.

2otb


Resolution: 1.47→10 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.261 3426 -Random
Rwork0.19 ---
obs0.192 68738 94.7 %-
all-68960 --
Displacement parametersBiso mean: 20.51 Å2
Refinement stepCycle: LAST / Resolution: 1.47→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3433 0 4 450 3887
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.029
X-RAY DIFFRACTIONc_bond_d0.009
LS refinement shellResolution: 1.47→1.52 Å

+
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