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- PDB-2pox: Dark state structure of the reversibly switchable fluorescent pro... -

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Basic information

Entry
Database: PDB / ID: 2pox
TitleDark state structure of the reversibly switchable fluorescent protein Dronpa
ComponentsFluorescent protein DronpaFluorescence
KeywordsFLUORESCENT PROTEIN / Luminescent protein / reversibly switchable fluorescent protein / green-fluorescent protein-like protein
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy / metal ion binding / identical protein 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
Fluorescent protein Dronpa
Similarity search - Component
Biological speciesEchinophyllia sp. SC22 (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.946 Å
AuthorsTrowitzsch, S. / Weber, G. / Wahl, M.C.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structural basis for reversible photoswitching in Dronpa
Authors: Andresen, M. / Stiel, A.C. / Trowitzsch, S. / Weber, G. / Eggeling, C. / Wahl, M.C. / Hell, S.W. / Jakobs, S.
History
DepositionApr 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Apr 15, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: pdbx_unobs_or_zero_occ_atoms / reflns ...pdbx_unobs_or_zero_occ_atoms / reflns / reflns_shell / struct_conn / struct_ref_seq_dif
Item: _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs ..._reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs / _reflns_shell.number_unique_all / _reflns_shell.number_unique_obs / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fluorescent protein Dronpa
B: Fluorescent protein Dronpa
C: Fluorescent protein Dronpa
D: Fluorescent protein Dronpa


Theoretical massNumber of molelcules
Total (without water)116,9884
Polymers116,9884
Non-polymers00
Water16,448913
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.894, 107.504, 275.663
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-442-

HOH

DetailsBiological assembly is the tetramer formed by chains A, B, C and D

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Components

#1: Protein
Fluorescent protein Dronpa / Fluorescence


Mass: 29246.963 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Echinophyllia sp. SC22 (invertebrata) / Gene: Dronpa / Plasmid: pRSETb-Dronpa / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: Q5TLG6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 913 / 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: 2.31 Å3/Da / Density % sol: 46.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 22% PEG 3350, 140mM Mg(NO3)2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 26, 2006 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.946→30 Å / Num. all: 79713 / Num. obs: 79474 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 0 Å2 / Rsym value: 0.098 / Net I/σ(I): 15.1
Reflection shellResolution: 1.946→2.06 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 3 / Num. unique obs: 11810 / Rsym value: 0.605 / % possible all: 98.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IOV
Resolution: 1.946→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / SU B: 6.374 / SU ML: 0.099 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.155 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21612 3984 5 %RANDOM
Rwork0.17407 ---
all0.17621 75697 --
obs0.17621 75485 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 4.144 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2---0.51 Å20 Å2
3---0.62 Å2
Refinement stepCycle: LAST / Resolution: 1.946→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7024 0 0 913 7937
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227776
X-RAY DIFFRACTIONr_angle_refined_deg1.491.95610572
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6835982
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.66724.74384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.683151321
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8081531
X-RAY DIFFRACTIONr_chiral_restr0.0970.21054
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026199
X-RAY DIFFRACTIONr_nbd_refined0.2020.23551
X-RAY DIFFRACTIONr_nbtor_refined0.3040.25208
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2819
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.242
X-RAY DIFFRACTIONr_mcbond_it0.3711.54836
X-RAY DIFFRACTIONr_mcangle_it0.64527624
X-RAY DIFFRACTIONr_scbond_it1.57933362
X-RAY DIFFRACTIONr_scangle_it2.554.52948
LS refinement shellResolution: 1.946→1.997 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 272 -
Rwork0.214 5339 -
obs--96.26 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.0337-0.0236-0.29750.66250.19221.60620.00640.24260.0844-0.0961-0.00450.0738-0.0986-0.114-0.0020.0090.0179-0.03420.04650.0115-0.1476-10.55331.37219.046
20.9597-0.0055-0.1560.86360.18071.43150.0205-0.03870.0020.0633-0.05660.0236-0.0355-0.12480.0361-0.05990.00350.0063-0.0202-0.0138-0.1458-13.23919.54947.769
31.1571-0.02140.07980.95440.07061.40950.0280.224-0.0801-0.11080.0297-0.14590.06990.2187-0.0577-0.04340.0040.01170.0462-0.0171-0.094124.02916.54432.509
40.8671-0.04590.16040.80870.0131.5281-0.0522-0.02750.1649-0.03230.0109-0.0012-0.21760.03090.04130.0155-0.0208-0.0492-0.0276-0.0012-0.084515.37141.70348.434
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-2 - 21831 - 249
2X-RAY DIFFRACTION2BB-2 - 21931 - 250
3X-RAY DIFFRACTION3CC1 - 21834 - 249
4X-RAY DIFFRACTION4DD2 - 21835 - 249

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