[English] 日本語
Yorodumi
- PDB-1zgq: Crystal Structure of the Discosoma Red Fluorescent Protein (DsRed... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1zgq
TitleCrystal Structure of the Discosoma Red Fluorescent Protein (DsRed) Variant Q66M
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
DI(HYDROXYETHYL)ETHER / Red fluorescent protein drFP583
Similarity search - Component
Biological speciesDiscosoma sp. (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
Remark 999SEQUENCE RESIDUES MET 66, TYR 67, GLY 68 ARE MODIFIED TO MAKE THE CHROMOPHORE NRQ 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
E: Red fluorescent protein drFP583
F: Red fluorescent protein drFP583
G: Red fluorescent protein drFP583
H: Red fluorescent protein drFP583
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,46216
Polymers207,6138
Non-polymers8498
Water28,1751564
1
A: Red fluorescent protein drFP583
B: Red fluorescent protein drFP583
C: Red fluorescent protein drFP583
D: Red fluorescent protein drFP583
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,3379
Polymers103,8074
Non-polymers5315
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14460 Å2
ΔGint-33 kcal/mol
Surface area32040 Å2
MethodPISA
2
E: Red fluorescent protein drFP583
F: Red fluorescent protein drFP583
G: Red fluorescent protein drFP583
H: Red fluorescent protein drFP583
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,1257
Polymers103,8074
Non-polymers3183
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13670 Å2
ΔGint-41 kcal/mol
Surface area32360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.235, 87.981, 161.639
Angle α, β, γ (deg.)90.00, 96.72, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Red fluorescent protein drFP583 / DsRed


Mass: 25951.666 Da / Num. of mol.: 8 / Mutation: Q66M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Discosoma sp. (sea anemone) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q9U6Y8
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1564 / 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: 2.52 Å3/Da / Density % sol: 50.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: PEG 8000, sodium chloride, phosphate-citrate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.999 / Wavelength: 0.999 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 162657 / Num. obs: 157512 / % possible obs: 97 % / Observed criterion σ(F): 0 / Rsym value: 0.064 / Net I/σ(I): 10
Reflection shellResolution: 1.9→1.97 Å / Mean I/σ(I) obs: 1.8 / Rsym value: 0.417 / % possible all: 88.6

-
Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→37.78 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 230636.49 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.22 7494 5 %RANDOM
Rwork0.194 ---
all0.194 157512 --
obs0.194 148662 91.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 12.5442 Å2 / ksol: 0.312782 e/Å3
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 1.9→37.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14330 0 0 1620 15950
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.54
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.21.5
X-RAY DIFFRACTIONc_mcangle_it3.532
X-RAY DIFFRACTIONc_scbond_it4.532
X-RAY DIFFRACTIONc_scangle_it7.072.5
LS refinement shellHighest resolution: 1.9 Å / Total num. of bins used: 6 /
Num. reflection% reflection
Rwork19679 -
Rfree-5.1 %

+
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