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- PDB-3cfh: Photoswitchable red fluorescent protein psRFP, off-state -

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Basic information

Entry
Database: PDB / ID: 3cfh
TitlePhotoswitchable red fluorescent protein psRFP, off-state
Components(GFP-like photoswitchable fluorescent protein) x 2
KeywordsFLUORESCENT PROTEIN / beta barrel / beta can / chromophore / photoactivation
Function / homology
Function and homology information


Pantoate--beta-alanine Ligase; Chain: A,domain 2 - #40 / Pantoate--beta-alanine Ligase; Chain: A,domain 2 / Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GFP-like non-fluorescent chromoprotein FP595
Similarity search - Component
Biological speciesAnemonia sulcata (snake-locks sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsKachalova, G.S. / Gundel, S. / Bartunik, H.D. / Wiedenmann, J.
CitationJournal: To be Published
Title: Structure of red fluorescent protein asRFP
Authors: Gundel, S. / Kachalova, G.S. / Oswald, F. / Fuchs, J. / Bartunik, H.D. / Nienhaus, G.U. / Wiedenmann, J.
History
DepositionMar 3, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_validate_polymer_linkage ...database_2 / pdbx_validate_polymer_linkage / struct_conn / struct_ref_seq_dif
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_ref_seq_dif.details
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: GFP-like photoswitchable fluorescent protein
A: GFP-like photoswitchable fluorescent protein
M: GFP-like photoswitchable fluorescent protein
B: GFP-like photoswitchable fluorescent protein
R: GFP-like photoswitchable fluorescent protein
G: GFP-like photoswitchable fluorescent protein
S: GFP-like photoswitchable fluorescent protein
H: GFP-like photoswitchable fluorescent protein


Theoretical massNumber of molelcules
Total (without water)103,7348
Polymers103,7348
Non-polymers00
Water16,358908
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30860 Å2
ΔGint-143.8 kcal/mol
Surface area31070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.819, 97.851, 241.827
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThis protein consists of 4 protein chains (1-231) and inside each of them there is break between 62 and 66 as chromophore. The biological unit is tetramer.

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Components

#1: Protein
GFP-like photoswitchable fluorescent protein / psRFP


Mass: 6744.721 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anemonia sulcata (snake-locks sea anemone)
Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 DE3 / References: UniProt: Q9GZ28*PLUS
#2: Protein
GFP-like photoswitchable fluorescent protein / psRFP


Mass: 19188.787 Da / Num. of mol.: 4 / Mutation: S143G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anemonia sulcata (snake-locks sea anemone)
Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 DE3 / References: UniProt: Q9GZ28*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 908 / 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: 2.79 Å3/Da / Density % sol: 55.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1M TRIS, 65%(w/v) MPD, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 20, 2007 / Details: mirror
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. all: 115913 / Num. obs: 115191 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 32.3 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 19.1
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 4 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2 / Num. unique all: 5751 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CFA

3cfa


Resolution: 1.75→12.27 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.849 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2304 5784 5 %RANDOM
Rwork0.20212 ---
obs0.20358 109836 99.44 %-
all-115913 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.785 Å2
Baniso -1Baniso -2Baniso -3
1-1.7 Å20 Å20 Å2
2--1.26 Å20 Å2
3----2.97 Å2
Refinement stepCycle: LAST / Resolution: 1.75→12.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7581 0 0 908 8489
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0227842
X-RAY DIFFRACTIONr_angle_refined_deg1.0931.98910646
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9435995
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.4624.233352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82151328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3971531
X-RAY DIFFRACTIONr_chiral_restr0.0690.21068
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026105
X-RAY DIFFRACTIONr_nbd_refined0.2030.23934
X-RAY DIFFRACTIONr_nbtor_refined0.2990.25089
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.21063
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.280
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3040.255
X-RAY DIFFRACTIONr_mcbond_it0.5311.54805
X-RAY DIFFRACTIONr_mcangle_it0.91427549
X-RAY DIFFRACTIONr_scbond_it1.05433519
X-RAY DIFFRACTIONr_scangle_it1.6564.53046
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 418 -
Rwork0.315 7871 -
obs-7871 99.54 %

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