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- PDB-4hq9: Crystal structure of a green-to-red photoconvertible DRONPA, pcDR... -

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Basic information

Entry
Database: PDB / ID: 4hq9
TitleCrystal structure of a green-to-red photoconvertible DRONPA, pcDRONPA in the green-off-state
ComponentsFluorescent protein Dronpa
KeywordsFLUORESCENT PROTEIN / Green-to-red fluorescent protein / Dronpa / Beta-barrel
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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Fluorescent protein Dronpa
Similarity search - Component
Biological speciesEchinophyllia (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsNguyen Bich, N. / Van Meervelt, L.
CitationJournal: ACS Nano / Year: 2014
Title: Green-to-red photoconvertible Dronpa mutant for multimodal super-resolution fluorescence microscopy
Authors: Moeyaert, B. / Nguyen Bich, N. / De Zitter, E. / Rocha, S. / Clays, K. / Mizuno, H. / van Meervelt, L. / Hofkens, J. / Dedecker, P.
History
DepositionOct 25, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Apr 23, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Nov 8, 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Oct 30, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,56213
Polymers176,5996
Non-polymers9637
Water10,827601
1
A: Fluorescent protein Dronpa
B: Fluorescent protein Dronpa
hetero molecules

A: Fluorescent protein Dronpa
B: Fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,45710
Polymers117,7334
Non-polymers7256
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545x,-y-1,-z1
Buried area8170 Å2
ΔGint-16 kcal/mol
Surface area31370 Å2
MethodPISA
2
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)118,3338
Polymers117,7334
Non-polymers6014
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7700 Å2
ΔGint-16 kcal/mol
Surface area31180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.180, 103.550, 176.900
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
11A-512-

HOH

21B-401-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11CHAIN A AND (NAME C OR NAME CA OR NAME O OR NAME N) AND (RESID 5:60 OR RESID 66:217)
21CHAIN B AND (NAME C OR NAME CA OR NAME O OR NAME N) AND (RESID 5:60 OR RESID 66:217)
31CHAIN C AND (NAME C OR NAME CA OR NAME O OR NAME N) AND (RESID 5:60 OR RESID 66:217)
41CHAIN D AND (NAME C OR NAME CA OR NAME O OR NAME N) AND (RESID 5:60 OR RESID 66:217)
51CHAIN E AND (NAME C OR NAME CA OR NAME O OR NAME N) AND (RESID 5:60 OR RESID 66:217)
61CHAIN F AND (NAME C OR NAME CA OR NAME O OR NAME N) AND (RESID 5:60 OR RESID 66:217)

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALARGARGCHAIN A AND (NAME C OR NAME CA OR NAME O OR NAME N) AND (RESID 5:60 OR RESID 66:217)AA3 - 22139 - 255
12VALVALARGARGCHAIN A AND (NAME C OR NAME CA OR NAME O OR NAME N) AND (RESID 5:60 OR RESID 66:217)AA3 - 22139 - 255
13VALVALARGARGCHAIN A AND (NAME C OR NAME CA OR NAME O OR NAME N) AND (RESID 5:60 OR RESID 66:217)AA3 - 22139 - 255
14VALVALARGARGCHAIN A AND (NAME C OR NAME CA OR NAME O OR NAME N) AND (RESID 5:60 OR RESID 66:217)AA3 - 22139 - 255
21VALVALPROPROCHAIN B AND (NAME C OR NAME CA OR NAME O OR NAME N) AND (RESID 5:60 OR RESID 66:217)BB3 - 22039 - 254
22VALVALPROPROCHAIN B AND (NAME C OR NAME CA OR NAME O OR NAME N) AND (RESID 5:60 OR RESID 66:217)BB3 - 22039 - 254
23VALVALPROPROCHAIN B AND (NAME C OR NAME CA OR NAME O OR NAME N) AND (RESID 5:60 OR RESID 66:217)BB3 - 22039 - 254
24VALVALPROPROCHAIN B AND (NAME C OR NAME CA OR NAME O OR NAME N) AND (RESID 5:60 OR RESID 66:217)BB3 - 22039 - 254
31METMETPROPROCHAIN C AND (NAME C OR NAME CA OR NAME O OR NAME N) AND (RESID 5:60 OR RESID 66:217)CC1 - 22037 - 254
32METMETPROPROCHAIN C AND (NAME C OR NAME CA OR NAME O OR NAME N) AND (RESID 5:60 OR RESID 66:217)CC1 - 22037 - 254
33METMETPROPROCHAIN C AND (NAME C OR NAME CA OR NAME O OR NAME N) AND (RESID 5:60 OR RESID 66:217)CC1 - 22037 - 254
34METMETPROPROCHAIN C AND (NAME C OR NAME CA OR NAME O OR NAME N) AND (RESID 5:60 OR RESID 66:217)CC1 - 22037 - 254
41VALVALPROPROCHAIN D AND (NAME C OR NAME CA OR NAME O OR NAME N) AND (RESID 5:60 OR RESID 66:217)DD3 - 22039 - 254
42VALVALPROPROCHAIN D AND (NAME C OR NAME CA OR NAME O OR NAME N) AND (RESID 5:60 OR RESID 66:217)DD3 - 22039 - 254
43VALVALPROPROCHAIN D AND (NAME C OR NAME CA OR NAME O OR NAME N) AND (RESID 5:60 OR RESID 66:217)DD3 - 22039 - 254
44VALVALPROPROCHAIN D AND (NAME C OR NAME CA OR NAME O OR NAME N) AND (RESID 5:60 OR RESID 66:217)DD3 - 22039 - 254
51SERSERPROPROCHAIN E AND (NAME C OR NAME CA OR NAME O OR NAME N) AND (RESID 5:60 OR RESID 66:217)EE2 - 22038 - 254
52SERSERPROPROCHAIN E AND (NAME C OR NAME CA OR NAME O OR NAME N) AND (RESID 5:60 OR RESID 66:217)EE2 - 22038 - 254
53SERSERPROPROCHAIN E AND (NAME C OR NAME CA OR NAME O OR NAME N) AND (RESID 5:60 OR RESID 66:217)EE2 - 22038 - 254
54SERSERPROPROCHAIN E AND (NAME C OR NAME CA OR NAME O OR NAME N) AND (RESID 5:60 OR RESID 66:217)EE2 - 22038 - 254
61VALVALGLYGLYCHAIN F AND (NAME C OR NAME CA OR NAME O OR NAME N) AND (RESID 5:60 OR RESID 66:217)FF3 - 21839 - 252
62VALVALGLYGLYCHAIN F AND (NAME C OR NAME CA OR NAME O OR NAME N) AND (RESID 5:60 OR RESID 66:217)FF3 - 21839 - 252
63VALVALGLYGLYCHAIN F AND (NAME C OR NAME CA OR NAME O OR NAME N) AND (RESID 5:60 OR RESID 66:217)FF3 - 21839 - 252
64VALVALGLYGLYCHAIN F AND (NAME C OR NAME CA OR NAME O OR NAME N) AND (RESID 5:60 OR RESID 66:217)FF3 - 21839 - 252

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Components

#1: Protein
Fluorescent protein Dronpa / Green Fluorescent Protein


Mass: 29433.164 Da / Num. of mol.: 6 / Mutation: V60A, C62H, N94S, N102I, E218G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Echinophyllia (invertebrata) / Strain: SC22 / Gene: Dronpa / Production host: Escherichia coli (E. coli) / References: UniProt: Q5TLG6
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 601 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRESIDUE CYS 62 MUTATED TO HIS 62. HIS 62, TYR 63 AND GLY 64 CIRCULARIZED INTO ONE CHROMOPHORE, CR8.

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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: 1.794 Å3/Da / Density % sol: 31.436 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25%(w/v) PEG 3350, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 24, 2012
RadiationMonochromator: fixed-exit monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.07→64.429 Å / Num. all: 77126 / Num. obs: 77126 / % possible obs: 98.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 32.71 Å2
Reflection shellResolution: 2.07→2.18 Å / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHASESphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HQ8

4hq8


Resolution: 2.07→64.429 Å / Occupancy max: 1 / Occupancy min: 0.36 / SU ML: 0.33 / σ(F): 1.5 / Phase error: 24.49 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2345 3876 5.03 %RANDOM
Rwork0.1888 ---
all0.208 77126 --
obs0.1911 76988 98.38 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.387 Å2 / ksol: 0.352 e/Å3
Displacement parametersBiso max: 90.56 Å2 / Biso mean: 34.8872 Å2 / Biso min: 13.68 Å2
Baniso -1Baniso -2Baniso -3
1-5.6748 Å2-0 Å2-0 Å2
2---3.1051 Å20 Å2
3----2.5697 Å2
Refinement stepCycle: LAST / Resolution: 2.07→64.429 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10407 0 64 601 11072
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01110798
X-RAY DIFFRACTIONf_angle_d1.30814590
X-RAY DIFFRACTIONf_chiral_restr0.0971477
X-RAY DIFFRACTIONf_plane_restr0.0061897
X-RAY DIFFRACTIONf_dihedral_angle_d15.6554025
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A830X-RAY DIFFRACTIONPOSITIONAL0.07
12B830X-RAY DIFFRACTIONPOSITIONAL0.07
13C829X-RAY DIFFRACTIONPOSITIONAL0.06
14D831X-RAY DIFFRACTIONPOSITIONAL0.083
15E831X-RAY DIFFRACTIONPOSITIONAL0.064
16F831X-RAY DIFFRACTIONPOSITIONAL0.074
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.07-2.09520.34671390.29882609274899
2.0952-2.12180.3151350.27212586272199
2.1218-2.14970.3521310.26142573270498
2.1497-2.17910.30551450.26182561270698
2.1791-2.21030.3031450.26612575272098
2.2103-2.24330.32041320.24772560269298
2.2433-2.27830.33561500.26232555270598
2.2783-2.31570.30631420.23892596273899
2.3157-2.35560.30581310.23642613274499
2.3556-2.39840.3091440.23422605274999
2.3984-2.44460.29061540.22662560271498
2.4446-2.49450.32161400.21472596273699
2.4945-2.54870.28781360.21862613274999
2.5487-2.6080.30691110.21092608271999
2.608-2.67320.28151410.20422621276299
2.6732-2.74550.31251300.1972560269098
2.7455-2.82630.26391320.19872572270497
2.8263-2.91750.2611460.20262620276699
2.9175-3.02180.23021210.18492649277099
3.0218-3.14280.21861490.1872622277199
3.1428-3.28580.21171400.17532616275698
3.2858-3.4590.20941370.17482635277298
3.459-3.67570.21761410.17082599274098
3.6757-3.95950.17231510.1542663281499
3.9595-4.35790.1791380.14952671280999
4.3579-4.98830.16131440.13752651279598
4.9883-6.28390.21351280.1732677280597
6.2839-64.45970.23031430.19072746288995

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