[English] 日本語
Yorodumi
- PDB-2wsn: Structure of Enhanced Cyan Fluorescent Protein at physiological pH -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wsn
TitleStructure of Enhanced Cyan Fluorescent Protein at physiological pH
ComponentsGREEN FLUORESCENT PROTEIN
KeywordsFLUORESCENT PROTEIN / CHROMOPHORE / LUMINESCENCE / PHOTOPROTEIN
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
Green fluorescent protein
Similarity search - Component
Biological speciesAEQUOREA VICTORIA (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsLelimousin, M. / Noirclerc-Savoye, M. / Lazareno-Saez, C. / Paetzold, B. / Le Vot, S. / Chazal, R. / Macheboeuf, P. / Field, M.J. / Bourgeois, D. / Royant, A.
Citation
Journal: Biochemistry / Year: 2009
Title: Intrinsic Dynamics in Ecfp and Cerulean Control Fluorescence Quantum Yield.
Authors: Lelimousin, M. / Noirclerc-Savoye, M. / Lazareno-Saez, C. / Paetzold, B. / Le Vot, S. / Chazal, R. / Macheboeuf, P. / Field, M.J. / Bourgeois, D. / Royant, A.
#1: Journal: J.Mol.Biol. / Year: 2003
Title: Expansion of the Genetic Code Enables Design of a Novel "Gold" Class of Green Fluorescent Proteins.
Authors: Bae, J.H. / Rubini, M. / Jung, G. / Wiegand, G. / Seifert, M.H.J. / Azim, M.K. / Kim, J.S. / Zumbusch, A. / Holak, T.A. / Moroder, L. / Huber, R. / Budisa, N.
History
DepositionSep 8, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / struct_conn / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GREEN FLUORESCENT PROTEIN


Theoretical massNumber of molelcules
Total (without water)26,9201
Polymers26,9201
Non-polymers00
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.182, 62.720, 70.593
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein GREEN FLUORESCENT PROTEIN


Mass: 26920.393 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-238
Source method: isolated from a genetically manipulated source
Details: CHROMOPHORE RESULTING FROM AUTOCATALYTIC CYCLIZATION OF CONSECUTIVE AMINO ACID RESIDUES THR65, TRP66 AND GLY67.
Source: (gene. exp.) AEQUOREA VICTORIA (jellyfish) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 CODONPLUS(DE3) RIL / References: UniProt: P42212
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsGFP VARIANT

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 40 % / Description: NONE
Crystal growpH: 7.5 / Details: 19.5% PEG8000, 4% GLYCEROL, 1M HEPES PH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 13, 2005 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.37→40 Å / Num. obs: 45997 / % possible obs: 94.9 % / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.3
Reflection shellResolution: 1.37→1.42 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.3 / % possible all: 70.4

-
Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OXE

1oxe


Resolution: 1.37→35.29 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.976 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.18514 2317 5 %RANDOM
Rwork0.14023 ---
obs0.14248 43679 94.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20 Å2
2--0.09 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.37→35.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1776 0 0 224 2000
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222019
X-RAY DIFFRACTIONr_bond_other_d0.0020.021341
X-RAY DIFFRACTIONr_angle_refined_deg1.8531.9852780
X-RAY DIFFRACTIONr_angle_other_deg0.9593.0013313
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7855274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.42325.40898
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.15115350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.891156
X-RAY DIFFRACTIONr_chiral_restr0.1210.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022313
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02401
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_it1.8721.51211
X-RAY DIFFRACTIONr_mcbond_other0.6781.5490
X-RAY DIFFRACTIONr_mcangle_it2.70621992
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.1963808
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.8444.5768
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.68433360
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.37→1.406 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 117 -
Rwork0.207 2306 -
obs--68.56 %

+
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