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- PDB-4kpi: Rotational order-disorder structure of reversibly photoswitchable... -

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Basic information

Entry
Database: PDB / ID: 4kpi
TitleRotational order-disorder structure of reversibly photoswitchable red fluorescent protein rsTagRFP
ComponentsReversibly photoswitchable red fluorescent protein rsTagRFP
KeywordsFLUORESCENT PROTEIN / beta-barrel / order-disorder structure / red fluorescent protein / reversibly photoswitchable fluorescent protein
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / Beta Barrel / Mainly Beta / Fluorescent protein FP480
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsPletnev, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: The rotational order-disorder structure of the reversibly photoswitchable red fluorescent protein rsTagRFP.
Authors: Pletnev, S. / Subach, F.V. / Verkhusha, V.V. / Dauter, Z.
History
DepositionMay 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Reversibly photoswitchable red fluorescent protein rsTagRFP


Theoretical massNumber of molelcules
Total (without water)27,6391
Polymers27,6391
Non-polymers00
Water1,36976
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.697, 92.697, 53.121
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-344-

HOH

21A-346-

HOH

31A-347-

HOH

41A-373-

HOH

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Components

#1: Protein Reversibly photoswitchable red fluorescent protein rsTagRFP


Mass: 27639.455 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 blue / References: UniProt: D0VX33*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.3 Å3/Da / Density % sol: 45.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M ammonium nitrate 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→30 Å / Num. obs: 15284 / % possible obs: 94.4 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.046 / Χ2: 0.976 / Net I/σ(I): 15.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.58-1.644.10.5969900.795162.2
1.64-1.75.10.50313640.879186.3
1.7-1.7870.41715790.923198.4
1.78-1.877.30.25415810.925199.4
1.87-1.997.30.13415720.962199
1.99-2.147.30.08616101.048199.4
2.14-2.367.30.06616011.128199.7
2.36-2.77.30.04616160.972199.7
2.7-3.47.20.03916421.116199.9
3.4-306.80.02917290.835199.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXdev_1090refinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U8A

3u8a


Resolution: 1.58→29.313 Å / Occupancy max: 1 / Occupancy min: 0.48 / FOM work R set: 0.7526 / SU ML: 0.2 / σ(F): 0 / Phase error: 30.71 / Stereochemistry target values: ML
Details: The crystal with rotational order-disorder pathology is composed of tetramers with 222 symmetry incorporated into the lattice in two different ways, rotated 90 degrees with respect to each ...Details: The crystal with rotational order-disorder pathology is composed of tetramers with 222 symmetry incorporated into the lattice in two different ways, rotated 90 degrees with respect to each other around the crystal c-axis, with tetramer axes coincident with crystallographic 2-fold axes. The random distribution of alternatively oriented tetramers in the crystal creates the rotational Order-Disorder structure with statistically averaged I422 symmetry in which one tetramer overlaps with 90 degree rotated tetramer in the same physical space.
RfactorNum. reflection% reflection
Rfree0.2788 711 4.98 %
Rwork0.2248 --
obs0.2274 14283 88.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 51.72 Å2 / Biso mean: 14.7786 Å2 / Biso min: 2.17 Å2
Refinement stepCycle: LAST / Resolution: 1.58→29.313 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1786 0 0 76 1862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141830
X-RAY DIFFRACTIONf_angle_d1.7892473
X-RAY DIFFRACTIONf_chiral_restr0.083260
X-RAY DIFFRACTIONf_plane_restr0.008320
X-RAY DIFFRACTIONf_dihedral_angle_d15.918684
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5804-1.70240.2376770.19361373145046
1.7024-1.87370.3021700.20572907307797
1.8737-2.14480.2751550.18783024317999
2.1448-2.70190.27681540.230930553209100
2.7019-29.31840.27891550.243332133368100

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