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- PDB-3e5v: Crystal Structure Analysis of eqFP611 Double Mutant T122R, N143S -

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Basic information

Entry
Database: PDB / ID: 3e5v
TitleCrystal Structure Analysis of eqFP611 Double Mutant T122R, N143S
ComponentsRed fluorescent protein eqFP611
KeywordsFLUORESCENT PROTEIN / Chromophore / Luminescence / Photoprotein / d2RFP630 / cis-trans isomer / 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 / Resolution: 2.1 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 1.2Nov 23, 2011Group: Structure summary
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Oct 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 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 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:
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Assembly

Deposited unit
A: Red fluorescent protein eqFP611


Theoretical massNumber of molelcules
Total (without water)27,6621
Polymers27,6621
Non-polymers00
Water1,35175
1
A: Red fluorescent protein eqFP611

A: Red fluorescent protein eqFP611


Theoretical massNumber of molelcules
Total (without water)55,3232
Polymers55,3232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/61
Buried area4940 Å2
ΔGint-16 kcal/mol
Surface area18940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.536, 62.536, 208.022
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

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


Mass: 27661.570 Da / Num. of mol.: 1 / Mutation: T122R, N143S
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.: 75 / 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: 2.25 Å3/Da / Density % sol: 45.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 20, 2006 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 13944 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.074 / Χ2: 1.288 / Net I/σ(I): 10.6
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 3.4 / Num. unique all: 1185 / Χ2: 1.811 / % possible all: 81.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
TNTrefinement
PDB_EXTRACT3.006data extraction
BUSTER-TNT2.1.1refinement
RefinementStarting model: 1UIS

1uis


Resolution: 2.1→13.89 Å / Occupancy max: 1 / Occupancy min: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.278 695 5.01 %RANDOM
Rwork0.226 ---
all0.228 13944 --
obs0.228 13873 93.28 %-
Displacement parametersBiso max: 109.45 Å2 / Biso mean: 48.961 Å2 / Biso min: 30.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.746 Å20 Å20 Å2
2---0.746 Å20 Å2
3---1.492 Å2
Refinement stepCycle: LAST / Resolution: 2.1→13.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1826 0 0 75 1901
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00318982
X-RAY DIFFRACTIONt_angle_deg0.74225422
X-RAY DIFFRACTIONt_dihedral_angle_d22.2813790
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.004562
X-RAY DIFFRACTIONt_gen_planes0.012805
X-RAY DIFFRACTIONt_it0.906189820
X-RAY DIFFRACTIONt_nbd0.013195
LS refinement shellResolution: 2.1→2.23 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.303 127 6.15 %
Rwork0.251 1938 -
all0.254 2065 -
obs--93.28 %

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