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- PDB-4emq: Crystal structure of a single mutant of Dronpa, the green-on-stat... -

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Basic information

Entry
Database: PDB / ID: 4emq
TitleCrystal structure of a single mutant of Dronpa, the green-on-state PDM1-4
ComponentsFluorescent protein Dronpa
KeywordsFLUORESCENT PROTEIN / DRONPA / GFP-LIKE PROTEIN / REVERSIBLE PHOTOSWITCHABLE FLUORESCENT PROTEIN / BETA BARREL
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
DI(HYDROXYETHYL)ETHER / Fluorescent protein Dronpa
Similarity search - Component
Biological speciesEchinophyllia sp. SC22 (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsNgan, N.B. / Van Hecke, K. / Van Meervelt, L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structural basis for the influence of a single mutation K145N on the oligomerization and photoswitching rate of Dronpa.
Authors: Nguyen Bich, N. / Moeyaert, B. / Van Hecke, K. / Dedecker, P. / Mizuno, H. / Hofkens, J. / Van Meervelt, L.
History
DepositionApr 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Sep 13, 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_close_contact / 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.ptnr1_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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,80220
Polymers175,3916
Non-polymers2,41114
Water15,925884
1
A: Fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7083
Polymers29,2321
Non-polymers4772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5763
Polymers29,2321
Non-polymers3442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6824
Polymers29,2321
Non-polymers4513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5763
Polymers29,2321
Non-polymers3442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5763
Polymers29,2321
Non-polymers3442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6824
Polymers29,2321
Non-polymers4513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.539, 103.804, 177.255
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11D-514-

HOH

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Components

#1: Protein
Fluorescent protein Dronpa


Mass: 29231.885 Da / Num. of mol.: 6 / Mutation: K145N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Echinophyllia sp. SC22 (invertebrata) / Gene: Dronpa / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: Q5TLG6
#2: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 884 / 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: 1

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Sample preparation

CrystalDensity Matthews: 1.82 Å3/Da / Density % sol: 32.56 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% PEG 3350, 0.1M Hepes pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 7, 2011
RadiationMonochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→54.93 Å / Num. all: 75756 / Num. obs: 75756 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.95→2.21 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 4 / Rsym value: 0.518 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASESphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2z1o

2z1o


Resolution: 1.95→54.709 Å / SU ML: 0.25 / σ(F): 1.33 / Phase error: 24.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2324 4728 5.02 %
Rwork0.1835 --
obs0.186 94192 99.95 %
all-75756 -
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.569 Å2 / ksol: 0.365 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.4672 Å20 Å2-0 Å2
2--4.0512 Å20 Å2
3----7.5184 Å2
Refinement stepCycle: LAST / Resolution: 1.95→54.709 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10337 0 125 884 11346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910808
X-RAY DIFFRACTIONf_angle_d1.30314605
X-RAY DIFFRACTIONf_dihedral_angle_d15.384034
X-RAY DIFFRACTIONf_chiral_restr0.0971474
X-RAY DIFFRACTIONf_plane_restr0.0051899
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.97220.36621670.27752930X-RAY DIFFRACTION100
1.9722-1.99540.31441660.2572941X-RAY DIFFRACTION100
1.9954-2.01970.28991610.24422920X-RAY DIFFRACTION100
2.0197-2.04530.30011490.23253010X-RAY DIFFRACTION100
2.0453-2.07220.30441560.23782901X-RAY DIFFRACTION100
2.0722-2.10060.27861480.22942957X-RAY DIFFRACTION100
2.1006-2.13060.29681500.22262921X-RAY DIFFRACTION100
2.1306-2.16240.27541720.21442980X-RAY DIFFRACTION100
2.1624-2.19620.29031470.21772954X-RAY DIFFRACTION100
2.1962-2.23220.28121680.212953X-RAY DIFFRACTION100
2.2322-2.27070.27541520.19922933X-RAY DIFFRACTION100
2.2707-2.3120.23251480.19022991X-RAY DIFFRACTION100
2.312-2.35640.25521620.18972954X-RAY DIFFRACTION100
2.3564-2.40450.26561530.19542971X-RAY DIFFRACTION100
2.4045-2.45680.26051630.18662936X-RAY DIFFRACTION100
2.4568-2.5140.22591420.19342983X-RAY DIFFRACTION100
2.514-2.57680.29311370.1872995X-RAY DIFFRACTION100
2.5768-2.64650.23391520.18692970X-RAY DIFFRACTION100
2.6465-2.72440.23141580.18942970X-RAY DIFFRACTION100
2.7244-2.81230.27991590.18292977X-RAY DIFFRACTION100
2.8123-2.91280.24011540.19612990X-RAY DIFFRACTION100
2.9128-3.02940.26331530.18092993X-RAY DIFFRACTION100
3.0294-3.16730.22681510.17432994X-RAY DIFFRACTION100
3.1673-3.33430.19841550.16653005X-RAY DIFFRACTION100
3.3343-3.54310.231450.16363015X-RAY DIFFRACTION100
3.5431-3.81660.21611540.16142995X-RAY DIFFRACTION100
3.8166-4.20060.20361710.15593015X-RAY DIFFRACTION100
4.2006-4.80810.16141980.15012996X-RAY DIFFRACTION99
4.8081-6.05650.20681750.16453070X-RAY DIFFRACTION100
6.0565-54.73040.21481620.19473244X-RAY DIFFRACTION100

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