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- PDB-2z1o: Crystal structure of a photoswitchable GFP-like protein Dronpa in... -

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Basic information

Entry
Database: PDB / ID: 2z1o
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 / 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: 1.75 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
DepositionMay 10, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)103,1214
Polymers103,1214
Non-polymers00
Water20,2131122
1
A: Fluorescent protein Dronpa


Theoretical massNumber of molelcules
Total (without water)25,7801
Polymers25,7801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fluorescent protein Dronpa


Theoretical massNumber of molelcules
Total (without water)25,7801
Polymers25,7801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Fluorescent protein Dronpa


Theoretical massNumber of molelcules
Total (without water)25,7801
Polymers25,7801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Fluorescent protein Dronpa


Theoretical massNumber of molelcules
Total (without water)25,7801
Polymers25,7801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.492, 103.516, 122.866
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Fluorescent protein Dronpa / Photochromic GFP-like protein


Mass: 25780.180 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Echinophyllia sp. SC22 (invertebrata) / Gene: Dronpa / Plasmid: pET28a / 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.: 1122 / 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: 2.29 Å3/Da / Density % sol: 46.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 90% of 0.1M HEPES (pH = 7.5) solution with 20% PEG 10000, 8% ethylene glycol, 10% of 0.1 M Tris/HCl (pH = 8.5) solution, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 6, 2006
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 94532 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.06
Reflection shellResolution: 1.75→1.81 Å / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 5.87 / % possible all: 99.6

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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: 2Z6Z

2z6z


Resolution: 1.75→19.98 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 257175.25 / Data cutoff low absF: 0 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.197 4582 5 %RANDOM
Rwork0.168 ---
obs0.168 91378 96.2 %-
all-94532 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.0514 Å2 / ksol: 0.384784 e/Å3
Displacement parametersBiso mean: 21.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.78 Å20 Å20 Å2
2---5.96 Å20 Å2
3---7.75 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6930 0 0 1122 8052
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d26.1
X-RAY DIFFRACTIONc_improper_angle_d1.5
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.231 720 5.2 %
Rwork0.207 13234 -
obs--89.3 %
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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