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- PDB-3pj7: Crystal structure of far-red fluorescent protein Katushka crystal... -

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Basic information

Entry
Database: PDB / ID: 3pj7
TitleCrystal structure of far-red fluorescent protein Katushka crystallized at pH 8.5
ComponentsRed fluorescent protein eqFP578
KeywordsFLUORESCENT PROTEIN / Katushka / far-red fluorescent protein / beta-barrel / Biomarker / Mutant variant of eqFP578 / Met-Tyr-Gly chromophore
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 eqFP578
Function and homology information
Biological speciesEntacmaea quadricolor (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 8, 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: Red fluorescent protein eqFP578
B: Red fluorescent protein eqFP578
C: Red fluorescent protein eqFP578
D: Red fluorescent protein eqFP578


Theoretical massNumber of molelcules
Total (without water)103,9584
Polymers103,9584
Non-polymers00
Water8,323462
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12640 Å2
ΔGint-50 kcal/mol
Surface area31780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.353, 161.353, 74.486
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
Red fluorescent protein eqFP578


Mass: 25989.564 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: H3JQU6*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 462 / 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: 47.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 24% w/v PEG4000, 0.16 M MgCl2, 0.08 M TRIS hydrochloride pH 8.5, 20% v/v glycerol, 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: 1.8→30 Å / Num. obs: 88163 / % possible obs: 100 % / Redundancy: 5 % / Rmerge(I) obs: 0.096 / Χ2: 1.156 / Net I/σ(I): 8.4
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
1.8-1.864.987760.8671100
1.86-1.94587710.96311000.648
1.94-2.03587771.05711000.439
2.03-2.13587791.15511000.314
2.13-2.27588091.20111000.257
2.27-2.44587771.32311000.188
2.44-2.69587971.2911000.141
2.69-3.08588241.3411000.106
3.08-3.88588541.27511000.079
3.88-30589991.07811000.066

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→24.99 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.2551 / WRfactor Rwork: 0.1991 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.7706 / SU B: 4.779 / SU ML: 0.137 / SU R Cruickshank DPI: 0.1467 / SU Rfree: 0.1453 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2518 1649 2.1 %RANDOM
Rwork0.1958 ---
obs0.197 79769 97.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.2 Å2 / Biso mean: 34.6951 Å2 / Biso min: 10.94 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.85→24.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7119 0 0 462 7581
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0227362
X-RAY DIFFRACTIONr_angle_refined_deg2.1391.9949941
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.575894
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.52624.585325
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.36151298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9731524
X-RAY DIFFRACTIONr_chiral_restr0.1490.21036
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025592
X-RAY DIFFRACTIONr_nbd_refined0.2290.23345
X-RAY DIFFRACTIONr_nbtor_refined0.3190.24923
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2612
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1090.212
X-RAY DIFFRACTIONr_mcbond_it1.2841.54581
X-RAY DIFFRACTIONr_mcangle_it1.93527166
X-RAY DIFFRACTIONr_scbond_it2.98833232
X-RAY DIFFRACTIONr_scangle_it4.3214.52768
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 121 -
Rwork0.333 5842 -
all-5963 -
obs--99.98 %

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