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

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Basic information

Entry
Database: PDB / ID: 3pjb
TitleCrystal structure of red fluorescent protein eqFP578 crystallized at pH 4.0
ComponentsRed fluorescent protein eqFP578
KeywordsFLUORESCENT PROTEIN / eqFP578 / red fluorescent protein / beta-barrel / Biomarker / 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: 1.75 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 9, 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 27, 2013Group: Other
Revision 1.4Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3724
Polymers52,1882
Non-polymers1842
Water6,035335
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-23 kcal/mol
Surface area18170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.658, 104.658, 216.527
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: 26093.805 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: H3JQU7*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 3.28 Å3/Da / Density % sol: 62.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 2.4 M ammonium sulfate, pH 4.0, 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: 1.69→50 Å / Num. obs: 76637 / % possible obs: 97.3 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.062 / Χ2: 0.997 / Net I/σ(I): 13.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.69-1.7511.30.7471560.944192.6
1.75-1.8211.60.56273300.96194.8
1.82-1.911.30.36774371.031195.9
1.9-2110.23675121.102196.7
2-2.1310.60.17575781.109197.2
2.13-2.2910.40.14876221.069197.6
2.29-2.5210.20.11876931.005198.1
2.52-2.8910.30.08578760.974199.6
2.89-3.64120.05879980.9351100
3.64-50150.03484350.907199.8

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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: 1.75→34.749 Å / Occupancy max: 1 / Occupancy min: 0.16 / SU ML: 0.16 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2076 1392 2 %
Rwork0.1765 --
obs0.1771 69631 97.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.065 Å2 / ksol: 0.455 e/Å3
Displacement parametersBiso max: 78.55 Å2 / Biso mean: 27.6203 Å2 / Biso min: 10.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.4362 Å20 Å2-0 Å2
2--0.4362 Å2-0 Å2
3----0.8724 Å2
Refinement stepCycle: LAST / Resolution: 1.75→34.749 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3558 0 12 335 3905
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0127489
X-RAY DIFFRACTIONf_angle_d1.26913520
X-RAY DIFFRACTIONf_chiral_restr0.126538
X-RAY DIFFRACTIONf_plane_restr0.0061171
X-RAY DIFFRACTIONf_dihedral_angle_d15.2281894
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.81250.27061250.21146499662495
1.8125-1.88510.25881490.1986530667996
1.8851-1.97090.22751140.18196656677096
1.9709-2.07480.18611320.16776688682097
2.0748-2.20480.21691460.16796707685397
2.2048-2.3750.18751290.16076800692998
2.375-2.61390.20051480.16346838698698
2.6139-2.9920.19281670.173669617128100
2.992-3.76880.22351320.168871097241100
3.7688-34.75540.19011500.179674517601100

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