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- PDB-8sxc: Crystal Structure of Fluorescent Protein Fusion Red 2 -

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Basic information

Entry
Database: PDB / ID: 8sxc
TitleCrystal Structure of Fluorescent Protein Fusion Red 2
ComponentsFar-red Fluorescent Protein Fusion Red 2
KeywordsFLUORESCENT PROTEIN
Function / homologyNITRATE ION
Function and homology information
Biological speciesEntacmaea quadricolor (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsPletnev, S. / Pletneva, N. / Pletnev, V.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation23-24-00011 Russian Federation
CitationJournal: To Be Published
Title: Crystal Structure of Fluorescent Protein Fusion Red 2
Authors: Pletnev, S. / Pletneva, N. / Pletnev, V.
History
DepositionMay 21, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Far-red Fluorescent Protein Fusion Red 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2366
Polymers27,6451
Non-polymers5915
Water2,180121
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.155, 81.442, 42.539
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Far-red Fluorescent Protein Fusion Red 2


Mass: 27645.459 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entacmaea quadricolor (sea anemone) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.23 Å3/Da / Density % sol: 44.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% w/v PEG 6000, 1.0M LiCl, 0.1M HEPES, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 39722 / % possible obs: 99.2 % / Redundancy: 6.7 % / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.035 / Rrim(I) all: 0.092 / Χ2: 1.008 / Net I/σ(I): 9.7 / Num. measured all: 267152
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.5-1.554.30.90736410.6990.9070.4331.0110.58793
1.55-1.625.80.7139540.8430.9570.3060.7750.61499.7
1.62-1.696.80.54839480.9290.9810.2230.5930.672100
1.69-1.787.20.36739520.9660.9910.1470.3960.754100
1.78-1.897.20.23139450.9820.9950.0920.2490.895100
1.89-2.047.20.14240030.990.9980.0570.1531.162100
2.04-2.247.20.10539840.9940.9980.0420.1131.252100
2.24-2.567.20.09240150.9940.9980.0370.0991.36100
2.56-3.237.20.07840620.9950.9990.0310.0841.288100
3.23-306.80.07442180.9920.9980.0310.081.15999.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
SCALEPACKdata scaling
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→27.31 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.475 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21927 1194 3 %RANDOM
Rwork0.16089 ---
obs0.16253 38480 98.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.27 Å2
Baniso -1Baniso -2Baniso -3
1--3.04 Å2-0 Å2-0 Å2
2---1.52 Å20 Å2
3---4.56 Å2
Refinement stepCycle: 1 / Resolution: 1.5→27.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1825 0 39 122 1986
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0141929
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171731
X-RAY DIFFRACTIONr_angle_refined_deg1.9371.6992591
X-RAY DIFFRACTIONr_angle_other_deg1.0431.6814070
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.565235
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.40822.87294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.8815330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.017159
X-RAY DIFFRACTIONr_chiral_restr0.1020.2241
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022117
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02356
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4142.835925
X-RAY DIFFRACTIONr_mcbond_other3.3772.829924
X-RAY DIFFRACTIONr_mcangle_it3.6774.2491151
X-RAY DIFFRACTIONr_mcangle_other3.6774.2541152
X-RAY DIFFRACTIONr_scbond_it5.5123.351004
X-RAY DIFFRACTIONr_scbond_other5.5223.349998
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7464.811431
X-RAY DIFFRACTIONr_long_range_B_refined4.92733.7591988
X-RAY DIFFRACTIONr_long_range_B_other4.84433.4221963
X-RAY DIFFRACTIONr_rigid_bond_restr4.5633660
X-RAY DIFFRACTIONr_sphericity_free20.589585
X-RAY DIFFRACTIONr_sphericity_bonded15.64153656
LS refinement shellResolution: 1.502→1.541 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 72 -
Rwork0.304 2426 -
obs--85.31 %

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