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- PDB-2z6z: Crystal structure of a photoswitchable GFP-like protein Dronpa in... -

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Basic information

Entry
Database: PDB / ID: 2z6z
TitleCrystal structure of a photoswitchable GFP-like protein Dronpa in the bright-state
ComponentsFluorescent protein Dronpa
KeywordsFLUORESCENT PROTEIN / GFP-like Protein / photochromism
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: 1.8 Å
AuthorsKikuchi, A. / Jeyakanthan, J. / Taka, J. / Shiro, Y. / Mizuno, H. / Miyawaki, A.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Light-dependent regulation of structural flexibility in a photochromic fluorescent protein.
Authors: Mizuno, H. / Mal, T.K. / Walchli, M. / Kikuchi, A. / Fukano, T. / Ando, R. / Jeyakanthan, J. / Taka, J. / Shiro, Y. / Ikura, M. / Miyawaki, A.
History
DepositionAug 9, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / 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 / 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
Revision 2.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
E: Fluorescent protein Dronpa
F: Fluorescent protein Dronpa


Theoretical massNumber of molelcules
Total (without water)175,4826
Polymers175,4826
Non-polymers00
Water22,5911254
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
MethodPISA
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
MethodPISA
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
MethodPISA
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
MethodPISA
5
E: Fluorescent protein Dronpa


Theoretical massNumber of molelcules
Total (without water)29,2471
Polymers29,2471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Fluorescent protein Dronpa


Theoretical massNumber of molelcules
Total (without water)29,2471
Polymers29,2471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.435, 182.660, 72.952
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11E-418-

HOH

21E-419-

HOH

31F-391-

HOH

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Components

#1: Protein
Fluorescent protein Dronpa / GFP-like protein 22G / photochromic protein Dronpa


Mass: 29246.963 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Echinophyllia sp. SC22 (invertebrata) / Gene: Dronpa / Plasmid: pRSET / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: Q5TLG6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1254 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE RESIDUE 63 IN THIS SEQUENCE IS GYC, CROMOPHORE. ORIGINAL SEQUENCE IS CYS, TYR, GLY.

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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: 2.02 Å3/Da / Density % sol: 39.13 %
Crystal growTemperature: 293 K / Method: microbatch method / pH: 8.3
Details: 27-27.5 % PEG 4000, 1M LiCl2, 0.1M Tris/HCl (pH 8.3), Microbatch Method, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 21, 2004
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 132847 / Num. obs: 132847 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.087
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 3.38 / Num. unique all: 13173 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GGX

1ggx


Resolution: 1.8→19.94 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2988023.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.219 6602 5 %RANDOM
Rwork0.195 ---
obs0.195 132101 99.8 %-
all-132847 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.0342 Å2 / ksol: 0.32235 e/Å3
Displacement parametersBiso mean: 24.4 Å2
Baniso -1Baniso -2Baniso -3
1-3.05 Å20 Å20 Å2
2---2.64 Å20 Å2
3----0.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10469 0 0 1254 11723
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.41
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.28 1073 4.9 %
Rwork0.251 20695 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3GYC.paramGYC.top

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