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- PDB-4hq8: Crystal structure of a green-to-red photoconvertible DRONPA, pcDR... -

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Basic information

Entry
Database: PDB / ID: 4hq8
TitleCrystal structure of a green-to-red photoconvertible DRONPA, pcDRONPA in the green-on-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 / MOLECULAR REPLACEMENT / Resolution: 1.95 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 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)177,67612
Polymers176,5996
Non-polymers1,0776
Water21,4741192
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)118,93412
Polymers117,7334
Non-polymers1,2018
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area8630 Å2
ΔGint-16 kcal/mol
Surface area32230 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)118,2096
Polymers117,7334
Non-polymers4772
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8410 Å2
ΔGint-15 kcal/mol
Surface area32140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.378, 107.186, 180.183
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-544-

HOH

21A-630-

HOH

31B-473-

HOH

41F-425-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11CHAIN A AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 66:217)
21CHAIN B AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 66:217)
31CHAIN C AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 66:217)
41CHAIN D AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 66:217)
51CHAIN E AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 66:217)
61CHAIN F AND (NAME C OR NAME CA OR NAME N OR NAME O) 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
11SERSERARGARGCHAIN A AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 66:217)AA2 - 22138 - 255
12SERSERARGARGCHAIN A AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 66:217)AA2 - 22138 - 255
13SERSERARGARGCHAIN A AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 66:217)AA2 - 22138 - 255
14SERSERARGARGCHAIN A AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 66:217)AA2 - 22138 - 255
21METMETPROPROCHAIN B AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 66:217)BB1 - 22037 - 254
22METMETPROPROCHAIN B AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 66:217)BB1 - 22037 - 254
23METMETPROPROCHAIN B AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 66:217)BB1 - 22037 - 254
24METMETPROPROCHAIN B AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 66:217)BB1 - 22037 - 254
31SERSERPROPROCHAIN C AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 66:217)CC2 - 22038 - 254
32SERSERPROPROCHAIN C AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 66:217)CC2 - 22038 - 254
33SERSERPROPROCHAIN C AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 66:217)CC2 - 22038 - 254
34SERSERPROPROCHAIN C AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 66:217)CC2 - 22038 - 254
41SERSERPROPROCHAIN D AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 66:217)DD2 - 22038 - 254
42SERSERPROPROCHAIN D AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 66:217)DD2 - 22038 - 254
43SERSERPROPROCHAIN D AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 66:217)DD2 - 22038 - 254
44SERSERPROPROCHAIN D AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 66:217)DD2 - 22038 - 254
51ILEILEPROPROCHAIN E AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 66:217)EE4 - 22040 - 254
52ILEILEPROPROCHAIN E AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 66:217)EE4 - 22040 - 254
53ILEILEPROPROCHAIN E AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 66:217)EE4 - 22040 - 254
54ILEILEPROPROCHAIN E AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 66:217)EE4 - 22040 - 254
61VALVALARGARGCHAIN F AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 66:217)FF3 - 22139 - 255
62VALVALARGARGCHAIN F AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 66:217)FF3 - 22139 - 255
63VALVALARGARGCHAIN F AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 66:217)FF3 - 22139 - 255
64VALVALARGARGCHAIN F AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 66:217)FF3 - 22139 - 255

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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-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1192 / 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: 1.98 Å3/Da / Density % sol: 37.84 %
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: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 15, 2012
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→28.92 Å / Num. all: 101878 / Num. obs: 101878 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.2 % / Biso Wilson estimate: 22.53 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.096
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.676 / Mean I/σ(I) obs: 2.1 / Num. unique all: 14754 / Rsym value: 0.676 / % possible all: 99.3

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASESphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Z1O

2z1o


Resolution: 1.95→28.456 Å / Occupancy max: 1 / Occupancy min: 0.31 / SU ML: 0.25 / σ(F): 2 / Phase error: 24.62 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2351 5085 4.99 %RANDOM
Rwork0.184 ---
all0.199 101848 --
obs0.1866 101833 99.07 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.78 Å2 / ksol: 0.359 e/Å3
Displacement parametersBiso max: 86.06 Å2 / Biso mean: 26.2652 Å2 / Biso min: 8.35 Å2
Baniso -1Baniso -2Baniso -3
1--4.2269 Å20 Å2-0 Å2
2--10.0034 Å20 Å2
3----5.7765 Å2
Refinement stepCycle: LAST / Resolution: 1.95→28.456 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10427 0 39 1192 11658
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910858
X-RAY DIFFRACTIONf_angle_d1.28914705
X-RAY DIFFRACTIONf_chiral_restr0.0931492
X-RAY DIFFRACTIONf_plane_restr0.0061915
X-RAY DIFFRACTIONf_dihedral_angle_d15.6254044
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A828X-RAY DIFFRACTIONPOSITIONAL0.058
12B828X-RAY DIFFRACTIONPOSITIONAL0.058
13C830X-RAY DIFFRACTIONPOSITIONAL0.058
14D828X-RAY DIFFRACTIONPOSITIONAL0.053
15E825X-RAY DIFFRACTIONPOSITIONAL0.054
16F827X-RAY DIFFRACTIONPOSITIONAL0.051
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-1.97220.32961630.28713179334299
1.9722-1.99540.28351680.26343198336699
1.9954-2.01970.32671500.26063243339399
2.0197-2.04530.31481410.2443179332099
2.0453-2.07220.32231830.24093201338499
2.0722-2.10050.31831790.23943160333999
2.1005-2.13050.30061600.22843217337799
2.1305-2.16230.28761580.222631973355100
2.1623-2.19610.28271670.225832483415100
2.1961-2.23210.27971560.221331953351100
2.2321-2.27060.2661840.218832103394100
2.2706-2.31180.31031540.210732353389100
2.3118-2.35630.2841670.207532273394100
2.3563-2.40430.25261580.19632343392100
2.4043-2.45660.24571790.192631973376100
2.4566-2.51370.26561750.232263401100
2.5137-2.57650.27451770.201632283405100
2.5765-2.64610.24341640.203432403404100
2.6461-2.7240.27811550.198132413396100
2.724-2.81180.26921840.184132453429100
2.8118-2.91220.27151760.195932363412100
2.9122-3.02870.24411800.190532273407100
3.0287-3.16640.24091570.18743266342399
3.1664-3.3330.23211980.17623194339299
3.333-3.54150.18791700.16963239340999
3.5415-3.81440.21331590.15233281344099
3.8144-4.19710.17161850.14293239342499
4.1971-4.80190.16421720.12363232340498
4.8019-6.04040.16961670.13583264343197
6.0404-28.45930.20461990.18323270346994

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