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

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Basic information

Entry
Database: PDB / ID: 4hqc
TitleCrystal structure of a green-to-red photoconvertible DRONPA, pcDRONPA in the red-on-state
ComponentsFluorescent protein Dronpa
KeywordsFLUORESCENT PROTEIN / Green-to-red fluorescent protein / Dronpa mutant / 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: 2.05 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 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_chiral / pdbx_validate_torsion / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _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

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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)177,36612
Polymers176,5096
Non-polymers8576
Water17,258958
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)117,9736
Polymers117,6734
Non-polymers3002
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565x,-y+1,-z1
Buried area8340 Å2
ΔGint-16 kcal/mol
Surface area31510 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)118,3809
Polymers117,6734
Non-polymers7075
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8990 Å2
ΔGint-21 kcal/mol
Surface area31370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.212, 106.131, 178.929
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-556-

HOH

21B-336-

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 63:217)
21CHAIN B AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 63:217)
31CHAIN C AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 63:217)
41CHAIN D AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 63:217)
51CHAIN E AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 63:217)
61CHAIN F AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 63:217)

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 63:217)AA2 - 22138 - 255
12SERSERARGARGCHAIN A AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 63:217)AA2 - 22138 - 255
13SERSERARGARGCHAIN A AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 63:217)AA2 - 22138 - 255
14SERSERARGARGCHAIN A AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 63:217)AA2 - 22138 - 255
21VALVALPROPROCHAIN B AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 63:217)BB3 - 22039 - 254
22VALVALPROPROCHAIN B AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 63:217)BB3 - 22039 - 254
23VALVALPROPROCHAIN B AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 63:217)BB3 - 22039 - 254
24VALVALPROPROCHAIN B AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 63:217)BB3 - 22039 - 254
31VALVALPROPROCHAIN C AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 63:217)CC3 - 22039 - 254
32VALVALPROPROCHAIN C AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 63:217)CC3 - 22039 - 254
33VALVALPROPROCHAIN C AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 63:217)CC3 - 22039 - 254
34VALVALPROPROCHAIN C AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 63:217)CC3 - 22039 - 254
41SERSERPROPROCHAIN D AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 63:217)DD2 - 22038 - 254
42SERSERPROPROCHAIN D AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 63:217)DD2 - 22038 - 254
43SERSERPROPROCHAIN D AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 63:217)DD2 - 22038 - 254
44SERSERPROPROCHAIN D AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 63:217)DD2 - 22038 - 254
51VALVALPROPROCHAIN E AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 63:217)EE3 - 22039 - 254
52VALVALPROPROCHAIN E AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 63:217)EE3 - 22039 - 254
53VALVALPROPROCHAIN E AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 63:217)EE3 - 22039 - 254
54VALVALPROPROCHAIN E AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 63:217)EE3 - 22039 - 254
61SERSERARGARGCHAIN F AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 63:217)FF2 - 22138 - 255
62SERSERARGARGCHAIN F AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 63:217)FF2 - 22138 - 255
63SERSERARGARGCHAIN F AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 63:217)FF2 - 22138 - 255
64SERSERARGARGCHAIN F AND (NAME C OR NAME CA OR NAME N OR NAME O) AND (RESID 5:60 OR RESID 63:217)FF2 - 22138 - 255

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Components

#1: Protein
Fluorescent protein Dronpa / Green Fluorescent Protein


Mass: 29418.172 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-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 958 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE CYS 62 MUTATED TO HIS 62. HIS 62, TYR 63 AND GLY 64 CIRCULARIZED INTO ONE CHROMOPHORE, CR8. ...RESIDUE CYS 62 MUTATED TO HIS 62. HIS 62, TYR 63 AND GLY 64 CIRCULARIZED INTO ONE CHROMOPHORE, CR8. A LIGHT-INDUCED CLEAVAGE OCCURS IN THE MAIN CHAIN BETWEEN PHE 61-CR8 63, RESULTING IN A NFA 61 AND A CHROMOPHORE, IEY.

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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: 1.91 Å3/Da / Density % sol: 35.46 %
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: 2.05→29.82 Å / Num. all: 85855 / Num. obs: 85855 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 27.49 Å2
Reflection shellResolution: 2.05→2.16 Å / % possible all: 100

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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 / Resolution: 2.05→29.67 Å / Occupancy max: 1 / Occupancy min: 0.26 / SU ML: 0.29 / σ(F): 1.34 / Phase error: 24.1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2328 4293 5 %RANDOM
Rwork0.1785 ---
obs0.1813 85783 99.99 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.352 Å2 / ksol: 0.363 e/Å3
Displacement parametersBiso max: 98.46 Å2 / Biso mean: 29.9115 Å2 / Biso min: 9.21 Å2
Baniso -1Baniso -2Baniso -3
1-2.3303 Å20 Å2-0 Å2
2--3.2872 Å20 Å2
3----5.6174 Å2
Refinement stepCycle: LAST / Resolution: 2.05→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10578 0 57 958 11593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111006
X-RAY DIFFRACTIONf_angle_d1.29514885
X-RAY DIFFRACTIONf_chiral_restr0.0931487
X-RAY DIFFRACTIONf_plane_restr0.0061937
X-RAY DIFFRACTIONf_dihedral_angle_d15.5464125
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A842X-RAY DIFFRACTIONPOSITIONAL0.056
12B842X-RAY DIFFRACTIONPOSITIONAL0.056
13C839X-RAY DIFFRACTIONPOSITIONAL0.058
14D841X-RAY DIFFRACTIONPOSITIONAL0.054
15E843X-RAY DIFFRACTIONPOSITIONAL0.056
16F841X-RAY DIFFRACTIONPOSITIONAL0.052
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.05-2.07330.30741360.254626902826
2.0733-2.09770.33391530.264826962849
2.0977-2.12330.30511200.247226892809
2.1233-2.15010.33391420.239126602802
2.1501-2.17840.29681730.234126382811
2.1784-2.20820.28931480.235226792827
2.2082-2.23980.31191410.224227152856
2.2398-2.27320.28671400.219726612801
2.2732-2.30870.32711440.210527122856
2.3087-2.34650.28611420.217326492791
2.3465-2.3870.2811510.211127112862
2.387-2.43040.29211360.207926712807
2.4304-2.47710.2781190.20127282847
2.4771-2.52760.27681450.205526962841
2.5276-2.58260.26071330.196626912824
2.5826-2.64260.26681560.193327202876
2.6426-2.70860.26081320.198527092841
2.7086-2.78180.28181370.197226992836
2.7818-2.86360.28711260.202127452871
2.8636-2.9560.25011530.193726892842
2.956-3.06150.25631630.19426832846
3.0615-3.1840.26181340.187127332867
3.184-3.32870.21661510.180627062857
3.3287-3.50390.21211410.168227382879
3.5039-3.72310.19791690.158327262895
3.7231-4.00990.20221450.140827352880
4.0099-4.41220.18341280.128327912919
4.4122-5.0480.12411310.112627852916
5.048-6.34970.16931320.137728222954
6.3497-29.67280.20761720.192629233095

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