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- PDB-3pj5: Crystal structure of far-red fluorescent protein Katushka crystal... -

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Basic information

Entry
Database: PDB / ID: 3pj5
TitleCrystal structure of far-red fluorescent protein Katushka crystallized at pH 5.0
ComponentsRed fluorescent protein eqFP578
KeywordsFLUORESCENT PROTEIN / Katushka / far-red fluorescent protein / beta-barrel / biomarker / Mutant variant of eqFP578 / Met-Tyr-Gly chromophore
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
Red fluorescent protein eqFP578
Similarity search - Component
Biological speciesEntacmaea quadricolor (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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
Revision 1.3Mar 26, 2025Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_polymer_linkage / struct_conn / struct_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Red fluorescent protein eqFP578
B: Red fluorescent protein eqFP578
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3025
Polymers51,0142
Non-polymers2883
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-58 kcal/mol
Surface area18160 Å2
MethodPISA
2
A: Red fluorescent protein eqFP578
B: Red fluorescent protein eqFP578
hetero molecules

A: Red fluorescent protein eqFP578
B: Red fluorescent protein eqFP578
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,60410
Polymers102,0284
Non-polymers5766
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/61
Buried area12730 Å2
ΔGint-155 kcal/mol
Surface area32050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.364, 104.364, 217.984
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Red fluorescent protein eqFP578


Mass: 25506.984 Da / Num. of mol.: 2
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: H3JQU5*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.36 Å3/Da / Density % sol: 63.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.5 M ammonium sulfate, pH 5.0, 25% 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: 1.6→30 Å / Num. obs: 92719 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.106 / Χ2: 1.237 / Net I/σ(I): 10.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.667.20.71991160.9811100
1.66-1.727.30.52290960.9931100
1.72-1.87.30.36391370.9751100
1.8-1.97.30.23191581.0311100
1.9-2.027.30.16191511.1811100
2.02-2.177.30.13692281.4151100
2.17-2.397.40.11492171.4141100
2.39-2.747.30.10293131.4761100
2.74-3.457.30.09794141.4491100
3.45-306.90.09298891.427199.9

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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: 1.6→30 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.2385 / WRfactor Rwork: 0.1969 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.8581 / SU B: 1.383 / SU ML: 0.05 / SU R Cruickshank DPI: 0.0732 / SU Rfree: 0.0789 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2259 1850 2 %RANDOM
Rwork0.1871 ---
obs0.1879 90289 97.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 57.74 Å2 / Biso mean: 25.2911 Å2 / Biso min: 11.66 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3576 0 15 287 3878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223977
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.9995414
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8145508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.10524.637179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.14615714
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8231514
X-RAY DIFFRACTIONr_chiral_restr0.0960.2559
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023058
X-RAY DIFFRACTIONr_nbd_refined0.2450.21870
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22646
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2303
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2490.275
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0950.216
X-RAY DIFFRACTIONr_mcbond_it0.9751.52421
X-RAY DIFFRACTIONr_mcangle_it1.51223826
X-RAY DIFFRACTIONr_scbond_it2.12331789
X-RAY DIFFRACTIONr_scangle_it3.1744.51553
LS refinement shellResolution: 1.601→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 115 -
Rwork0.269 6588 -
all-6703 -
obs--99.73 %

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