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Basic information

Entry
Database: PDB / ID: 2iov
TitleBright-state structure of the reversibly switchable fluorescent protein Dronpa
ComponentsFluorescent protein Dronpa
KeywordsLUMINESCENT PROTEIN / reversibly switchable fluorescent protein / green-fluorescent protein-like protein
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy / identical protein binding / 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
Fluorescent protein Dronpa
Similarity search - Component
Biological speciesEchinophyllia sp. SC22 (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsStiel, A.C. / Trowitzsch, S. / Weber, G. / Andresen, M. / Eggeling, C. / Hell, S.W. / Jakobs, S. / Wahl, M.C.
CitationJournal: Biochem.J. / Year: 2007
Title: 1.8 A bright-state structure of the reversibly switchable fluorescent protein Dronpa guides the generation of fast switching variants
Authors: Stiel, A.C. / Trowitzsch, S. / Weber, G. / Andresen, M. / Eggeling, C. / Hell, S.W. / Jakobs, S. / Wahl, M.C.
History
DepositionOct 11, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 25, 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 / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif
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
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 / pdbx_validate_torsion / 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
Water15,907883
1
A: Fluorescent protein Dronpa


Theoretical massNumber of molelcules
Total (without water)29,2471
Polymers29,2471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fluorescent protein Dronpa


Theoretical massNumber of molelcules
Total (without water)29,2471
Polymers29,2471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Fluorescent protein Dronpa


Theoretical massNumber of molelcules
Total (without water)29,2471
Polymers29,2471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Fluorescent protein Dronpa


Theoretical massNumber of molelcules
Total (without water)29,2471
Polymers29,2471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.292, 109.627, 275.232
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
11C-355-

HOH

21D-425-

HOH

31D-465-

HOH

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Components

#1: Protein
Fluorescent protein Dronpa


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


Mass: 18.015 Da / Num. of mol.: 883 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES CYS 62, TYR 63 AND GLY 64 AUTOCATALYTICALLY FORM THE CHROMOPHORE GYC LABELLED AS RESIDUE ...RESIDUES CYS 62, TYR 63 AND GLY 64 AUTOCATALYTICALLY FORM THE CHROMOPHORE GYC LABELLED AS RESIDUE 62 IN THE COORDINATES.

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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: 2.43 Å3/Da / Density % sol: 49.3 %
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: 1.04025 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 8, 2005
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04025 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 99209 / Num. obs: 104290 / % possible obs: 83.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.2 % / Biso Wilson estimate: 21 Å2 / Rsym value: 0.07 / Net I/σ(I): 19.1
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 2333 / Rsym value: 0.452 / % possible all: 26.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345345DTBdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 2A50

2a50


Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 6.003 / SU ML: 0.095 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21636 5201 5 %RANDOM
Rwork0.18523 ---
obs0.18678 98948 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.716 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2--1.14 Å20 Å2
3----1.53 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7060 0 0 883 7943
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0227684
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3591.96210427
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5735952
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.81324.597372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.641151306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1471529
X-RAY DIFFRACTIONr_chiral_restr0.0950.21050
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026055
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1880.23504
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.25063
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2714
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.236
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6451.54762
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.01727491
X-RAY DIFFRACTIONr_scbond_it1.75233347
X-RAY DIFFRACTIONr_scangle_it2.6474.52936
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.799→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 353 -
Rwork0.281 7073 -
obs--96.34 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.38740.1159-0.00681.4706-0.13011.85490.0780.1420.1223-0.2427-0.03710.33720.09-0.3706-0.0409-0.04210.0425-0.0507-0.0181-0.0101-0.024113.89337.39532.456
20.9135-0.02970.04831.1797-0.17621.7520.1419-0.1402-0.1365-0.192-0.07560.11960.5237-0.0867-0.06630.2234-0.023-0.0175-0.1684-0.0009-0.112623.48112.38148.328
31.09160.10060.27860.8407-0.21862.4148-0.04390.255-0.0962-0.2824-0.0032-0.12160.51430.36830.04710.24740.16630.065-0.0583-0.0148-0.151648.79423.98318.714
40.93640.0440.18981.07190.09361.53640.01440.00030.01450.039-0.0523-0.07290.2170.26750.0379-0.02360.10290.0096-0.02060.0161-0.103751.57835.56147.812
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 21734 - 248
2X-RAY DIFFRACTION2BB2 - 21835 - 249
3X-RAY DIFFRACTION3CC-2 - 21831 - 249
4X-RAY DIFFRACTION4DD-1 - 21832 - 249

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