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- PDB-2gx0: Crystal structural and functional analysis of GFP-like fluorescen... -

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Basic information

Entry
Database: PDB / ID: 2gx0
TitleCrystal structural and functional analysis of GFP-like fluorescent protein
Componentsfluorescent protein Dronpa
KeywordsLUMINESCENT PROTEIN / fluorescence / b-can / photoswitching
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: 1.9 Å
AuthorsHwang, K.Y. / Nam, K.-H. / Park, S.-Y. / Sugiyama, K.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2007
Title: Structural characterization of the photoswitchable fluorescent protein Dronpa-C62S
Authors: Nam, K.-H. / Kwon, O.Y. / Sugiyama, K. / Lee, W.-H. / Kim, Y.K. / Song, H.K. / Kim, E.E. / Park, S.-Y. / Jeon, H. / Hwang, K.Y.
History
DepositionMay 8, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 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 / 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 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)110,4534
Polymers110,4534
Non-polymers00
Water10,989610
1
A: fluorescent protein Dronpa


Theoretical massNumber of molelcules
Total (without water)27,6131
Polymers27,6131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: fluorescent protein Dronpa


Theoretical massNumber of molelcules
Total (without water)27,6131
Polymers27,6131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: fluorescent protein Dronpa


Theoretical massNumber of molelcules
Total (without water)27,6131
Polymers27,6131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: fluorescent protein Dronpa


Theoretical massNumber of molelcules
Total (without water)27,6131
Polymers27,6131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8000 Å2
ΔGint-2 kcal/mol
Surface area31940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.595, 103.595, 122.326
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 / GFP-like fluorescent Protein


Mass: 27613.295 Da / Num. of mol.: 4 / Fragment: Green fluorescent protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Echinophyllia sp. SC22 (invertebrata) / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5TLG6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 610 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.81 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPAL/PLS 4A11
SYNCHROTRONPhoton Factory BL-5A21
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDMay 26, 2005
ADSC QUANTUM 3152CCDDec 23, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1150SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 68388 / Num. obs: 68388 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 8.6 Å2
Reflection shellResolution: 1.9→1.97 Å / % possible all: 66.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCdata collection
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XSS

1xss


Resolution: 1.9→20 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 89612.42 / 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
Rfree0.211 6900 10.1 %RANDOM
Rwork0.178 ---
obs0.178 68284 91.8 %-
all-68284 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 18.9079 Å2 / ksol: 0.34058 e/Å3
Displacement parametersBiso mean: 24.6 Å2
Baniso -1Baniso -2Baniso -3
1--5.51 Å20 Å20 Å2
2---7.04 Å20 Å2
3---12.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7011 0 0 610 7621
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.12
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: 1.9→2.02 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.249 865 10.2 %
Rwork0.209 7643 -
obs--69.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1proteinnam.paramproteinnam.top
X-RAY DIFFRACTION2cyg.paramcyg.top
X-RAY DIFFRACTION3water.paramwater.top

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