[English] 日本語
- PDB-2fzu: Reduced enolate chromophore intermediate for GFP variant -

Open data

ID or keywords:


Basic information

Database: PDB / ID: 2fzu
TitleReduced enolate chromophore intermediate for GFP variant
ComponentsGreen fluorescent protein
KeywordsLUMINESCENT PROTEIN / chromophore / intermediate / biosynthesis / post-translational modification / high resolution
Function / homology
Function and homology information

bioluminescence / generation of precursor metabolites and energy / protein-chromophore linkage
Green fluorescent protein, GFP / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Green Fluorescent Protein / Beta Barrel / Mainly Beta
Green fluorescent protein
Biological speciesAequorea victoria (jellyfish)
AuthorsBarondeau, D.P. / Tainer, J.A. / Getzoff, E.D.
CitationJournal: J.Am.Chem.Soc. / Year: 2006
Title: Structural evidence for an enolate intermediate in GFP fluorophore biosynthesis.
Authors: Barondeau, D.P. / Tainer, J.A. / Getzoff, E.D.
Validation Report
SummaryFull reportAbout validation report
DepositionFeb 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 999SEQUENCE Ser 65 in the database has been mutated to THR. The residues THR 65, TYR 66 and GLY 67 ...SEQUENCE Ser 65 in the database has been mutated to THR. The residues THR 65, TYR 66 and GLY 67 constitute the chromophore C12 66.

Structure visualization

Structure viewerMolecule:

Downloads & links


Deposited unit
A: Green fluorescent protein
hetero molecules

Theoretical massNumber of molelcules
Total (without water)26,9073

TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.350, 62.520, 71.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe monomer in the assymetric unit is the biological assembly


#1: Protein Green fluorescent protein /

Mass: 26820.145 Da / Num. of mol.: 1 / Mutation: F64L, S65T, F99S, M153T, V163A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P42212
#2: Chemical ChemComp-MG / MAGNESIUM ION / Magnesium

Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol

Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water

Mass: 18.015 Da / Num. of mol.: 356 / Source method: isolated from a natural source / Formula: H2O

Experimental details


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

Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50 mM MgCl2, 50 mM Hepes, 20% PEG 4K, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 28, 2000
RadiationMonochromator: Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.25→20 Å / Num. all: 154670 / Num. obs: 62613 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 9.9 Å2 / Rsym value: 0.045 / Net I/σ(I): 19.6
Reflection shellResolution: 1.25→1.29 Å / Mean I/σ(I) obs: 2.3 / Rsym value: 0.349 / % possible all: 91.5


DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ema
Resolution: 1.25→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.199 3116 Random
Rwork0.142 --
All0.142 62451 -
Obs-59335 -
Refinement stepCycle: LAST / Resolution: 1.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1919 0 11 350 2280
Refine LS restraints
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.022
X-RAY DIFFRACTIONs_angle_d0.032

About Yorodumi


Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices

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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.:Changes in new EM Navigator and Yorodumi

Read more


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.

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