[English] 日本語
Yorodumi
- PDB-1zgo: High Resolution Crystal Structure of the Discosoma Red Fluorescen... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1zgo
TitleHigh Resolution Crystal Structure of the Discosoma Red Fluorescent Protein (DsRed)
ComponentsRed fluorescent protein drFP583
KeywordsLUMINESCENT PROTEIN / RFP / red / fluorescent protein / DsRed / drFP583 / chromophore / GFP / coral / beta barrel / 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
Red fluorescent protein drFP583
Similarity search - Component
Biological speciesDiscosoma sp. (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsTubbs, J.L. / Tainer, J.A. / Getzoff, E.D.
CitationJournal: Biochemistry / Year: 2005
Title: Crystallographic structures of discosoma red fluorescent protein with immature and mature chromophores: linking Peptide bond trans-cis isomerization and acylimine formation in chromophore maturation.
Authors: Tubbs, J.L. / Tainer, J.A. / Getzoff, E.D.
History
DepositionApr 21, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn / struct_ref_seq_dif
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details
Revision 2.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE RESIDUES GLN 66, TYR 67, GLY 68 ARE MODIFIED TO MAKE THE CHROMOPHORE CRQ 66.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Red fluorescent protein drFP583
B: Red fluorescent protein drFP583
C: Red fluorescent protein drFP583
D: Red fluorescent protein drFP583


Theoretical massNumber of molelcules
Total (without water)103,7944
Polymers103,7944
Non-polymers00
Water9,638535
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9340 Å2
ΔGint-31 kcal/mol
Surface area31780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.717, 127.221, 57.118
Angle α, β, γ (deg.)90.00, 100.42, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Red fluorescent protein drFP583 / DsRed


Mass: 25948.600 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Discosoma sp. (sea anemone) / Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q9U6Y8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 535 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 35.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: MPD, HEPES, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationMonochromator: Single crystal Si(220); cylindrically bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→40 Å / Num. all: 153198 / Num. obs: 148353 / % possible obs: 96.8 % / Rsym value: 0.051 / Net I/σ(I): 18
Reflection shellResolution: 1.4→1.45 Å / Mean I/σ(I) obs: 1.9 / Rsym value: 0.357 / % possible all: 93.2

-
Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→40 Å / Num. parameters: 69807 / Num. restraintsaints: 88146 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: The Phe 65-Crq 66 peptide bond has been refined as a mixture of two conformations: the standard trans conformation and the cis conformation, unique to the mature DsRed chromophore.
RfactorNum. reflection% reflectionSelection details
Rfree0.206 7039 -RANDOM
Rwork0.143 ---
all0.143 140833 --
obs0.143 132400 92 %-
Refine analyzeNum. disordered residues: 16 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 7683.85
Refinement stepCycle: LAST / Resolution: 1.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7219 0 0 535 7754
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0295
X-RAY DIFFRACTIONs_zero_chiral_vol0.049
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.066
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.054
X-RAY DIFFRACTIONs_approx_iso_adps0.069

+
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