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- PDB-4q7t: Crystal structure of photoswitchable fluorescent protein PSmOrange -

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Basic information

Entry
Database: PDB / ID: 4q7t
TitleCrystal structure of photoswitchable fluorescent protein PSmOrange
ComponentsPSmOrange
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: 1.94 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: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
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: PSmOrange
B: PSmOrange


Theoretical massNumber of molelcules
Total (without water)56,4202
Polymers56,4202
Non-polymers00
Water2,882160
1
A: PSmOrange


Theoretical massNumber of molelcules
Total (without water)28,2101
Polymers28,2101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PSmOrange


Theoretical massNumber of molelcules
Total (without water)28,2101
Polymers28,2101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.363, 50.683, 52.414
Angle α, β, γ (deg.)94.710, 90.030, 106.590
Int Tables number1
Space group name H-MP1

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Components

#1: Protein PSmOrange


Mass: 28209.912 Da / Num. of mol.: 2 / Mutation: S12T, Q64L, F99Y, L124M, K162R, P186S
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES PHE65, 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: 2.04 Å3/Da / Density % sol: 39.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 55% MPD, 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: Aug 19, 2010
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: 1.94→52.221 Å / Num. obs: 27702 / % possible obs: 84.5 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.055 / Χ2: 0.922 / Net I/σ(I): 9.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.94-1.982.90.1769400.538156.6
1.98-2.023.10.1949900.551161.6
2.02-2.063.10.16311040.583166.5
2.06-2.13.20.15311410.576169.6
2.1-2.153.20.14911810.605173.3
2.15-2.23.20.14312940.61177.3
2.2-2.253.20.13613140.583181.9
2.25-2.313.20.11914490.628187
2.31-2.383.20.10915000.628191.4
2.38-2.463.30.1115440.667195.1
2.46-2.543.30.09215820.665196.5
2.54-2.653.40.08815840.735197.1
2.65-2.773.30.0716160.817197.3
2.77-2.913.30.06215840.85196.9
2.91-3.13.30.05515810.916196.6
3.1-3.333.30.04715481.124194.7
3.33-3.673.20.04414791.357189.9
3.67-4.23.20.04214271.599187.4
4.2-5.293.20.0413411.742182
5.29-52.2213.40.04215032.074191.4

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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: 1.94→52.22 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.2682 / WRfactor Rwork: 0.2028 / FOM work R set: 0.7879 / SU B: 4.84 / SU ML: 0.138 / SU R Cruickshank DPI: 0.2325 / SU Rfree: 0.2064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.233 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2656 1387 5 %RANDOM
Rwork0.1998 ---
obs0.203 26506 84.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 108.91 Å2 / Biso mean: 43.276 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--3.96 Å22.28 Å2-0.48 Å2
2--6.49 Å2-0.56 Å2
3----1.31 Å2
Refinement stepCycle: LAST / Resolution: 1.94→52.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3498 0 0 160 3658
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.023609
X-RAY DIFFRACTIONr_angle_refined_deg2.1531.9754864
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3795432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.68323.976166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.55815641
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.891519
X-RAY DIFFRACTIONr_chiral_restr0.1260.2488
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212767
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 90 -
Rwork0.231 1243 -
all-1333 -
obs--54.99 %

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