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- PDB-3lf3: Crystal Structure of Fast Fluorescent Timer Fast-FT -

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Basic information

Entry
Database: PDB / ID: 3lf3
TitleCrystal Structure of Fast Fluorescent Timer Fast-FT
ComponentsFast Fluorescent Timer Fast-FT
KeywordsFLUORESCENT PROTEIN / Fluorescent Timers / Blue-to-red conversion / Chromophore degradation
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
Biological speciesDiscosoma sp. (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsPletnev, S. / Dauter, Z.
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: Understanding blue-to-red conversion in monomeric fluorescent timers and hydrolytic degradation of their chromophores
Authors: Pletnev, S. / Subach, F.V. / Dauter, Z. / Wlodawer, A. / Verkhusha, V.V.
History
DepositionJan 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fast Fluorescent Timer Fast-FT


Theoretical massNumber of molelcules
Total (without water)26,3331
Polymers26,3331
Non-polymers00
Water7,098394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.838, 42.517, 61.766
Angle α, β, γ (deg.)90.00, 112.07, 90.00
Int Tables number4
Space group name H-MP1211
DetailsMonomer

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Components

#1: Protein Fast Fluorescent Timer Fast-FT


Mass: 26332.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Discosoma sp. (sea anemone) / Production host: Escherichia coli (E. coli) / Strain (production host): LMG194 / References: UniProt: D1MPT3*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H2O
Compound detailsIN THIS FLUORESCENT PROTEIN THE CHROMOPHORE MOIETY FORMED FROM RESIDUES MET66-TYR67-GLY68, (NRQ66), ...IN THIS FLUORESCENT PROTEIN THE CHROMOPHORE MOIETY FORMED FROM RESIDUES MET66-TYR67-GLY68, (NRQ66), UNDERGOES HYDROLYTIC DEGRADATION ON ~80% WHICH RESULT IN MET66 BEING COMPLETELY REMOVED FROM POLYPEPTIDE CHAIN AND PHE65 BEING AMIDATED TO GIVE PHENILALANINEAMIDE (NFA65). DEGRADED CHROMOPHORE MOIETY IS COMPOSED OF RESIDUES TYR67-GLY68 ONLY.

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M MgCl2, 0.1M Tris, 30% w/v PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.15→30 Å / Num. obs: 83298 / % possible obs: 99.7 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.048 / Χ2: 0.986 / Net I/σ(I): 11.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.15-1.192.70.45780750.96297.3
1.19-1.243.30.41482731.00799.8
1.24-1.33.60.32783360.977100
1.3-1.363.60.24683280.986100
1.36-1.453.70.16682910.957100
1.45-1.563.70.1183531.034100
1.56-1.723.70.07983501.039100
1.72-1.973.80.0583771.002100
1.97-2.483.80.03383841.011100
2.48-303.70.03485310.87699.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.005data extraction
SERGUIdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.15→29.762 Å / Occupancy max: 1 / Occupancy min: 0.09 / FOM work R set: 0.926 / SU ML: 0.16 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.177 1668 2 %
Rwork0.149 --
obs0.15 83201 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.577 Å2 / ksol: 0.397 e/Å3
Displacement parametersBiso max: 59.37 Å2 / Biso mean: 15.536 Å2 / Biso min: 6.82 Å2
Baniso -1Baniso -2Baniso -3
1--1.004 Å20 Å20.654 Å2
2--2.14 Å20 Å2
3----1.136 Å2
Refinement stepCycle: LAST / Resolution: 1.15→29.762 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2017 0 0 394 2411
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112093
X-RAY DIFFRACTIONf_angle_d1.5382843
X-RAY DIFFRACTIONf_chiral_restr0.103274
X-RAY DIFFRACTIONf_plane_restr0.009383
X-RAY DIFFRACTIONf_dihedral_angle_d15.839821
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.15-1.1840.2071350.1996592672797
1.184-1.2220.1791450.18167326877100
1.222-1.2660.1831280.15667656893100
1.266-1.3160.1661500.1467686918100
1.316-1.3760.1471350.12668116946100
1.376-1.4490.1411390.11267596898100
1.449-1.540.1321610.10967966957100
1.54-1.6580.1561570.11367636920100
1.658-1.8250.1591280.12568386966100
1.825-2.0890.1621480.12268567004100
2.089-2.6320.1741190.13968686987100
2.632-29.7720.1961230.16569857108100

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