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- PDB-3e5t: Crystal Structure Analysis of FP611 -

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Basic information

Entry
Database: PDB / ID: 3e5t
TitleCrystal Structure Analysis of FP611
ComponentsRed fluorescent protein eqFP611
KeywordsFLUORESCENT PROTEIN / Chromophore / Luminescence / Photoprotein / red fluorescent protein
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / Beta Barrel / Mainly Beta / Red fluorescent protein eqFP611
Function and homology information
Biological speciesEntacmaea quadricolor (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.1 Å
AuthorsNar, H. / Nienhaus, K. / Nienhaus, U. / Wiedenmann, J.
CitationJournal: J.Am.Chem.Soc. / Year: 2008
Title: Trans-cis isomerization is responsible for the red-shifted fluorescence in variants of the red fluorescent protein eqFP611.
Authors: Nienhaus, K. / Nar, H. / Heilker, R. / Wiedenmann, J. / Nienhaus, G.U.
History
DepositionAug 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Red fluorescent protein eqFP611


Theoretical massNumber of molelcules
Total (without water)27,6341
Polymers27,6341
Non-polymers00
Water8,251458
1
A: Red fluorescent protein eqFP611

A: Red fluorescent protein eqFP611


Theoretical massNumber of molelcules
Total (without water)55,2692
Polymers55,2692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area4760 Å2
ΔGint-14 kcal/mol
Surface area18600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.638, 69.416, 41.369
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1388-

HOH

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Components

#1: Protein Red fluorescent protein eqFP611 / GFP-like chromoprotein / FP611


Mass: 27634.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entacmaea quadricolor (sea anemone)
Description: synonymous source organism name Parasicyonis actinostoloides
Production host: Escherichia coli (E. coli) / Strain (production host): M15pREP4 / References: UniProt: Q8ISF8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / Source method: isolated from a natural source / Formula: H2O

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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: 2.33 Å3/Da / Density % sol: 47.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 8000, pH 4.6, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 24, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.1→10 Å / Num. all: 87481 / Num. obs: 71928 / % possible obs: 92.6 % / Observed criterion σ(F): 4 / Rmerge(I) obs: 0.048 / Net I/σ(I): 26
Reflection shellResolution: 1.1→1.14 Å / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 3 / % possible all: 82.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
SHELXrefinement
PDB_EXTRACT3.006data extraction
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UIS

1uis


Resolution: 1.1→10 Å / Occupancy max: 1 / Occupancy min: 0.25 / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.168 4609 random
Rwork0.116 --
all0.131 87481 -
obs-71928 -
Displacement parametersBiso max: 115.95 Å2 / Biso mean: 22.821 Å2 / Biso min: 7.64 Å2
Refinement stepCycle: LAST / Resolution: 1.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2084 0 0 458 2542
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.021
X-RAY DIFFRACTIONs_angle_d0.035

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