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Basic information

Entry
Database: PDB / ID: 2gx2
TitleCrystal structural and functional analysis of GFP-like fluorescent protein Dronpa
Componentsfluorescent protein DronpaFluorescence
KeywordsLUMINESCENT PROTEIN / photoswiching / fluorescence 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
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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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
E: fluorescent protein Dronpa
F: fluorescent protein Dronpa
G: fluorescent protein Dronpa
H: fluorescent protein Dronpa
I: fluorescent protein Dronpa
J: fluorescent protein Dronpa
K: fluorescent protein Dronpa
L: fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)332,67474
Polymers331,16712
Non-polymers1,50762
Water36,6062032
1
A: fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7437
Polymers27,5971
Non-polymers1466
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7929
Polymers27,5971
Non-polymers1948
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7929
Polymers27,5971
Non-polymers1948
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7678
Polymers27,5971
Non-polymers1707
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7678
Polymers27,5971
Non-polymers1707
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7196
Polymers27,5971
Non-polymers1225
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6704
Polymers27,5971
Non-polymers733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6945
Polymers27,5971
Non-polymers974
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6945
Polymers27,5971
Non-polymers974
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
J: fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6222
Polymers27,5971
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
11
K: fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7437
Polymers27,5971
Non-polymers1466
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
12
L: fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6704
Polymers27,5971
Non-polymers733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.091, 106.160, 110.070
Angle α, β, γ (deg.)61.17, 70.85, 86.21
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
fluorescent protein Dronpa / Fluorescence / GFP-like fluorescent protein


Mass: 27597.229 Da / Num. of mol.: 12 / 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: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 62 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2032 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE DIFFERENCE BETWEEN THE SEQUENCE DATABASE AND THE COORDINATES IS THAT GYS 62 REPRESENTS THE ...THE DIFFERENCE BETWEEN THE SEQUENCE DATABASE AND THE COORDINATES IS THAT GYS 62 REPRESENTS THE CHROMOPHORE (SER-TYR-GLY). IN ADDITION, SER 62 HAS BEEN MUTATED FROM CYS WHICH OCCURS NATURALLY.

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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: 2.12 Å3/Da / Density % sol: 42.01 %
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: 1.8→50 Å / Num. all: 707315 / Num. obs: 236555 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 11.5 Å2
Reflection shellResolution: 1.8→1.86 Å / % possible all: 81.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCdata collection
HKL-2000data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GX0

2gx0


Resolution: 1.8→19.99 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 131119.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.209 11796 5 %RANDOM
Rwork0.182 ---
obs0.182 236384 93.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 21.0317 Å2 / ksol: 0.347704 e/Å3
Displacement parametersBiso mean: 23.4 Å2
Baniso -1Baniso -2Baniso -3
1-5.65 Å22.56 Å2-3.35 Å2
2---3.39 Å2-0.28 Å2
3----2.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20941 0 62 2032 23035
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_d1.1
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: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.286 1755 5.2 %
Rwork0.257 32312 -
obs--81.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1proteinsyg.parproteinsyg.top
X-RAY DIFFRACTION2syg.parsyg.top
X-RAY DIFFRACTION3water.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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