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- PDB-4q7u: Crystal structure of photoswitchable fluorescent protein PSmOrange2 -

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Basic information

Entry
Database: PDB / ID: 4q7u
TitleCrystal structure of photoswitchable fluorescent protein PSmOrange2
ComponentsPSmOrange2
KeywordsFLUORESCENT PROTEIN / beta-barrel / photoswitchable fluorescent protein / chromophore
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy / metal ion binding
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
Biological speciesDiscosoma sp. (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsMalashkevich, V.N. / Pletnev, S. / Almo, S.C.
CitationJournal: Plos One / Year: 2014
Title: Orange Fluorescent Proteins: Structural Studies of LSSmOrange, PSmOrange and PSmOrange2.
Authors: Pletnev, S. / Shcherbakova, D.M. / Subach, O.M. / Pletneva, N.V. / Malashkevich, V.N. / Almo, S.C. / Dauter, Z. / Verkhusha, V.V.
History
DepositionApr 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_validate_polymer_linkage / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 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: PSmOrange2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2452
Polymers28,1531
Non-polymers921
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.724, 43.874, 52.544
Angle α, β, γ (deg.)90.000, 94.370, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PSmOrange2


Mass: 28152.859 Da / Num. of mol.: 1
Mutation: R17H, S12T, R36H, Q64L, F65I, F99Y, L124M, K162R, P186S, Q188L, A217S, G219A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Discosoma sp. (sea anemone) / Production host: Escherichia coli (E. coli) / Strain (production host): LMG194 / References: UniProt: D0VWW2
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE PHE65 WAS MUTATED TO ILE. RESIDUES ILE65, GLY66, TYR67, AND GLY68 CIRCULARIZED INTO ONE CHROMOPHORE.

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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: 1.87 Å3/Da / Density % sol: 34.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, PEG1000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.08 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 19, 2011
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.3→52.391 Å / Num. obs: 49302 / % possible obs: 96.4 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.05 / Χ2: 1.066 / Net I/σ(I): 12.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.3-1.322.20.36117280.841167.5
1.32-1.352.30.33919900.903177.6
1.35-1.372.50.33422240.95188.3
1.37-1.42.80.29424260.934196.1
1.4-1.433.50.26525620.9971100
1.43-1.463.60.22725261.0311100
1.46-1.53.60.225431.0881100
1.5-1.543.60.16625521.0991100
1.54-1.593.60.14225451.1361100
1.59-1.643.60.12725431.2421100
1.64-1.73.70.11325561.2411100
1.7-1.763.70.09525551.221100
1.76-1.843.70.07725371.3521100
1.84-1.943.70.06225381.4081100
1.94-2.063.70.05125731.192199.9
2.06-2.223.70.04925531.089199.9
2.22-2.453.60.05225740.909199.9
2.45-2.83.60.04925580.946199.8
2.8-3.533.50.03326000.76199.7
3.53-52.3913.50.02626190.597198.8

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.14data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2H5O

2h5o


Resolution: 1.3→52.39 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.1726 / WRfactor Rwork: 0.1433 / FOM work R set: 0.9129 / SU B: 1.438 / SU ML: 0.028 / SU R Cruickshank DPI: 0.0553 / SU Rfree: 0.0507 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.055 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.1767 2525 5.1 %RANDOM
Rwork0.148 ---
obs0.1494 49286 96.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 57.48 Å2 / Biso mean: 13.616 Å2 / Biso min: 5.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20.44 Å2
2---0.3 Å20 Å2
3---0.45 Å2
Refinement stepCycle: LAST / Resolution: 1.3→52.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1757 0 6 211 1974
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022004
X-RAY DIFFRACTIONr_angle_refined_deg1.5881.982737
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3995266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.85624.06691
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.77615372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1431510
X-RAY DIFFRACTIONr_chiral_restr0.0840.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211567
X-RAY DIFFRACTIONr_rigid_bond_restr2.14432004
X-RAY DIFFRACTIONr_sphericity_free19.199555
X-RAY DIFFRACTIONr_sphericity_bonded5.47752086
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 117 -
Rwork0.225 2453 -
all-2570 -
obs--68.79 %

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