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- PDB-3pib: Crystal structure of red fluorescent protein eqFP578 crystallized... -

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Basic information

Entry
Database: PDB / ID: 3pib
TitleCrystal structure of red fluorescent protein eqFP578 crystallized at pH 5.5
ComponentseqFP578 fluorescent protein
KeywordsFLUORESCENT PROTEIN / Red fluorescent protein / beta-barrel / biomarker / Met-Tyr-Gly chromophore / sea anemone
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / Beta Barrel / Mainly Beta / eqFP578 fluorescent protein
Function and homology information
Biological speciesEntacmaea quadricolor (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.154 Å
AuthorsPletnev, S. / Pletneva, N.V. / Pletnev, V.Z.
CitationJournal: Protein Sci. / Year: 2011
Title: Crystallographic study of red fluorescent protein eqFP578 and its far-red variant Katushka reveals opposite pH-induced isomerization of chromophore.
Authors: Pletneva, N.V. / Pletnev, V.Z. / Shemiakina, I.I. / Chudakov, D.M. / Artemyev, I. / Wlodawer, A. / Dauter, Z. / Pletnev, S.
History
DepositionNov 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: eqFP578 fluorescent protein
B: eqFP578 fluorescent protein
C: eqFP578 fluorescent protein
D: eqFP578 fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,1118
Polymers107,7424
Non-polymers3684
Water12,989721
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: eqFP578 fluorescent protein
D: eqFP578 fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0554
Polymers53,8712
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-25 kcal/mol
Surface area18240 Å2
MethodPISA
3
B: eqFP578 fluorescent protein
C: eqFP578 fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0554
Polymers53,8712
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-20 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.247, 161.247, 75.682
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

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Components

#1: Protein
eqFP578 fluorescent protein


Mass: 26935.617 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entacmaea quadricolor (sea anemone) / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: H3JQU4*PLUS
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 721 / 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: 2.28 Å3/Da / Density % sol: 46.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25% w/v PEG 3350, 0.2 M ammonium acetate, 0.1 M BIS-TRIS pH 5.5., 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 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.15→50 Å / Num. obs: 314590 / % possible obs: 91.6 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.055 / Χ2: 1.056 / Net I/σ(I): 9.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.15-1.194.70.488204600.83159.9
1.19-1.245.10.44265950.853177.5
1.24-1.35.20.388296680.894186.8
1.3-1.365.40.318324050.936194.5
1.36-1.455.50.26339281.007199
1.45-1.565.60.176339671.105199.1
1.56-1.725.80.115341391.138199.5
1.72-1.9760.078343231.221199.9
1.97-2.486.30.048344411.1481100
2.48-506.20.033346641.155199.6

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.1data extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.154→35.915 Å / Occupancy max: 1 / Occupancy min: 0.04 / SU ML: 0.12 / σ(F): 1.34
RfactorNum. reflection% reflection
Rfree0.1765 3201 1.02 %
Rwork0.1546 --
obs0.1549 314461 92.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.794 Å2 / ksol: 0.417 e/Å3
Displacement parametersBiso max: 58.79 Å2 / Biso mean: 17.0049 Å2 / Biso min: 5.76 Å2
Baniso -1Baniso -2Baniso -3
1--2.7709 Å2-0 Å20 Å2
2---2.7709 Å20 Å2
3---5.5418 Å2
Refinement stepCycle: LAST / Resolution: 1.154→35.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7320 0 24 721 8065
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0138018
X-RAY DIFFRACTIONf_angle_d1.68110920
X-RAY DIFFRACTIONf_chiral_restr0.0931138
X-RAY DIFFRACTIONf_plane_restr0.0091423
X-RAY DIFFRACTIONf_dihedral_angle_d17.4393092
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.154-1.17120.2233930.18849459955265
1.1712-1.18960.24291120.1676104001051272
1.1896-1.20910.22731100.1689108611097175
1.2091-1.22990.17641160.1596114371155379
1.2299-1.25230.22781180.1644121101222883
1.2523-1.27640.21621060.1597126191272586
1.2764-1.30240.19891250.1547131481327390
1.3024-1.33070.20261500.1555136201377094
1.3307-1.36170.15621400.1489139761411696
1.3617-1.39570.20571570.1521143181447598
1.3957-1.43350.19431410.1475144711461299
1.4335-1.47570.20061520.1373144591461199
1.4757-1.52330.16561450.1245144891463499
1.5233-1.57770.12721720.1141144271459999
1.5777-1.64090.16871320.1134144651459799
1.6409-1.71560.15921580.11751458114739100
1.7156-1.8060.14381490.12571450814657100
1.806-1.91920.15871680.13791458614754100
1.9192-2.06730.13511490.13451462614775100
2.0673-2.27540.15821520.14271459314745100
2.2754-2.60450.14421520.15111467714829100
2.6045-3.28110.19661450.16811466514810100
3.2811-35.93210.18551590.1684147651492499

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