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- PDB-3zuj: Padron on (fluorescent) ABcis -

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Basic information

Entry
Database: PDB / ID: 3zuj
TitlePadron on (fluorescent) ABcis
ComponentsFLUORESCENT PROTEIN DRONPA
KeywordsFLUORESCENT PROTEIN / GFP VARIANTS / POSITIVE PHOTOSWITCHING / FPS / RSFPS / CRYO-PROBE / INTERMEDIATE STATE / ISOMERIZATION
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
Fluorescent protein Dronpa
Similarity search - Component
Biological speciesECHINOPHYLLIA SP. SC22 (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.345 Å
AuthorsREGIS Faro, A. / Carpentier, P. / Bourgeois, D.
CitationJournal: J.Am.Chem.Soc. / Year: 2011
Title: Low-Temperature Chromophore Isomerization Reveals the Photoswitching Mechanism of the Fluorescent Protein Padron.
Authors: Regis Faro, A. / Carpentier, P. / Jonasson, G. / Pompidor, G. / Arcizet, D. / Demachy, I. / Bourgeois, D.
History
DepositionJul 19, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2011Group: Database references / Other / Structure summary
Revision 1.2Oct 23, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / struct_conn / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_torsion / struct_conn / struct_sheet
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id / _struct_sheet.number_strands
Revision 2.1Dec 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 12-STRANDED BARREL THIS IS REPRESENTED BY A 13-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 12-STRANDED BARREL THIS IS REPRESENTED BY A 13-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 12-STRANDED BARREL THIS IS REPRESENTED BY A 13-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 12-STRANDED BARREL THIS IS REPRESENTED BY A 13-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 12-STRANDED BARREL THIS IS REPRESENTED BY A 13-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "FA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 12-STRANDED BARREL THIS IS REPRESENTED BY A 13-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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


Theoretical massNumber of molelcules
Total (without water)147,1126
Polymers147,1126
Non-polymers00
Water9,620534
1
A: FLUORESCENT PROTEIN DRONPA


Theoretical massNumber of molelcules
Total (without water)24,5191
Polymers24,5191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FLUORESCENT PROTEIN DRONPA


Theoretical massNumber of molelcules
Total (without water)24,5191
Polymers24,5191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: FLUORESCENT PROTEIN DRONPA


Theoretical massNumber of molelcules
Total (without water)24,5191
Polymers24,5191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: FLUORESCENT PROTEIN DRONPA


Theoretical massNumber of molelcules
Total (without water)24,5191
Polymers24,5191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: FLUORESCENT PROTEIN DRONPA


Theoretical massNumber of molelcules
Total (without water)24,5191
Polymers24,5191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: FLUORESCENT PROTEIN DRONPA


Theoretical massNumber of molelcules
Total (without water)24,5191
Polymers24,5191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.580, 181.560, 72.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11C-2002-

HOH

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Components

#1: Protein
FLUORESCENT PROTEIN DRONPA / PADRON


Mass: 24518.703 Da / Num. of mol.: 6 / Fragment: RESIDUES 2-217
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ECHINOPHYLLIA SP. SC22 (invertebrata) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q5TLG6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 534 / 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: 2.48 Å3/Da / Density % sol: 50.45 % / Description: NONE
Crystal growpH: 7.5
Details: 500 MM MG(NO3)2, 50 MM HEPES (PH 7.5), 26% PEG 3350 AS CRYSTALLIZATION BUFFER. OPTIMIZED CRYSTALS WERE THEN OBTAINED BY MICRO-SEEDING IN THE SAME BUFFER, EXCEPT THAT A REDUCED AMOUNT OF PEG 3350 WAS USED (16%).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 23, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.34→50 Å / Num. obs: 61045 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 5.23 % / Biso Wilson estimate: 26.63 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.91
Reflection shellResolution: 2.34→2.49 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 5.29 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Z1O

2z1o


Resolution: 2.345→46.544 Å / SU ML: 0.83 / σ(F): 1.99 / Phase error: 24.34 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2502 1998 3.3 %
Rwork0.1886 --
obs0.1906 61026 98.88 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 18.431 Å2 / ksol: 0.321 e/Å3
Displacement parametersBiso mean: 26.5 Å2
Baniso -1Baniso -2Baniso -3
1-9.8592 Å20 Å20 Å2
2---6.0959 Å20 Å2
3----3.7632 Å2
Refinement stepCycle: LAST / Resolution: 2.345→46.544 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10324 0 0 534 10858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811041
X-RAY DIFFRACTIONf_angle_d1.26114984
X-RAY DIFFRACTIONf_dihedral_angle_d15.0354109
X-RAY DIFFRACTIONf_chiral_restr0.0791496
X-RAY DIFFRACTIONf_plane_restr0.0051988
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3451-2.40380.34761380.2474065X-RAY DIFFRACTION97
2.4038-2.46880.3181420.22974206X-RAY DIFFRACTION100
2.4688-2.54140.28591430.20434219X-RAY DIFFRACTION100
2.5414-2.62340.34591430.21054207X-RAY DIFFRACTION100
2.6234-2.71720.25151420.19664207X-RAY DIFFRACTION100
2.7172-2.8260.27421430.19244213X-RAY DIFFRACTION100
2.826-2.95450.34131440.20274240X-RAY DIFFRACTION100
2.9545-3.11030.30191420.21124209X-RAY DIFFRACTION100
3.1103-3.30510.24591450.19324289X-RAY DIFFRACTION100
3.3051-3.56020.25141440.19884239X-RAY DIFFRACTION100
3.5602-3.91830.31871280.22123814X-RAY DIFFRACTION89
3.9183-4.48490.18291440.14074242X-RAY DIFFRACTION99
4.4849-5.6490.14731470.12964355X-RAY DIFFRACTION100
5.649-46.55320.20571530.19114523X-RAY DIFFRACTION100

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