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- PDB-3zul: Padron on (fluorescent) Icis intermediate state -

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Basic information

Entry
Database: PDB / ID: 3zul
TitlePadron on (fluorescent) Icis intermediate state
ComponentsFLUORESCENT PROTEIN DRONPA
KeywordsFLUORESCENT PROTEIN / GFP VARIANTS / POSITIVE / PHOTOSWITCHING / FPS / RSFPS / CRYO-PROBE / ISOMERIZATION
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
Fluorescent protein Dronpa
Similarity search - Component
Biological speciesECHINOPHYLLIA SP. SC22 (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFaro, A.R. / Carpentier, P. / Bougeois, 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 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / 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: Advisory / Atomic model ...Advisory / 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_unobs_or_zero_occ_atoms / 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_sheet.number_strands
Revision 2.1Dec 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
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)152,0626
Polymers152,0626
Non-polymers00
Water9,224512
1
A: FLUORESCENT PROTEIN DRONPA


Theoretical massNumber of molelcules
Total (without water)25,3441
Polymers25,3441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FLUORESCENT PROTEIN DRONPA


Theoretical massNumber of molelcules
Total (without water)25,3441
Polymers25,3441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: FLUORESCENT PROTEIN DRONPA


Theoretical massNumber of molelcules
Total (without water)25,3441
Polymers25,3441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: FLUORESCENT PROTEIN DRONPA


Theoretical massNumber of molelcules
Total (without water)25,3441
Polymers25,3441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: FLUORESCENT PROTEIN DRONPA


Theoretical massNumber of molelcules
Total (without water)25,3441
Polymers25,3441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: FLUORESCENT PROTEIN DRONPA


Theoretical massNumber of molelcules
Total (without water)25,3441
Polymers25,3441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.970, 181.380, 72.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
FLUORESCENT PROTEIN DRONPA / PADRON


Mass: 25343.674 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ECHINOPHYLLIA SP. SC22 (invertebrata) / Variant: SYNTHETIC CONSTRUCT / Plasmid: PRSET / 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.: 512 / Source method: isolated from a natural source / Formula: H2O

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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: 2.46 Å3/Da / Density % sol: 50.12 % / 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 CCD / Detector: CCD / Date: Feb 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 64825 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 22.73 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.4
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.1 / % possible all: 98.4

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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: 2.3→46.517 Å / SU ML: 0.81 / σ(F): 1.99 / Phase error: 25.75 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.256 2000 3.1 %
Rwork0.2042 --
obs0.2058 64688 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 14.061 Å2 / ksol: 0.317 e/Å3
Displacement parametersBiso mean: 23.9 Å2
Baniso -1Baniso -2Baniso -3
1-5.156 Å20 Å20 Å2
2---5.2195 Å20 Å2
3---0.0635 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.517 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10314 0 0 512 10826
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910981
X-RAY DIFFRACTIONf_angle_d1.24314893
X-RAY DIFFRACTIONf_dihedral_angle_d16.4594058
X-RAY DIFFRACTIONf_chiral_restr0.0811502
X-RAY DIFFRACTIONf_plane_restr0.0041956
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.35760.36541410.26934420X-RAY DIFFRACTION100
2.3576-2.42130.30391420.24064459X-RAY DIFFRACTION100
2.4213-2.49260.28761400.23164398X-RAY DIFFRACTION100
2.4926-2.5730.35391430.23634444X-RAY DIFFRACTION100
2.573-2.6650.30371400.23554428X-RAY DIFFRACTION100
2.665-2.77170.3391430.22494443X-RAY DIFFRACTION100
2.7717-2.89780.26441410.21954464X-RAY DIFFRACTION100
2.8978-3.05050.26571440.2224478X-RAY DIFFRACTION100
3.0505-3.24160.27451420.20994452X-RAY DIFFRACTION100
3.2416-3.49180.25261430.21544501X-RAY DIFFRACTION100
3.4918-3.84310.28181400.21184373X-RAY DIFFRACTION97
3.8431-4.39880.18541430.16264509X-RAY DIFFRACTION100
4.3988-5.54060.16571470.14194590X-RAY DIFFRACTION100
5.5406-46.52620.22541510.19554729X-RAY DIFFRACTION99

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