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- PDB-3tmr: IrisFP, planar chromophore -

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Basic information

Entry
Database: PDB / ID: 3tmr
TitleIrisFP, planar chromophore
ComponentsGreen to red photoconvertible GPF-like protein EosFP
KeywordsFLUORESCENT PROTEIN / Beta-can
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
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
SULFITE ION / Green to red photoconvertible GFP-like protein EosFP
Similarity search - Component
Biological speciesLobophyllia hemprichii (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAdam, V. / Carpentier, P. / Roy, A. / Field, M. / Bourgeois, D.
CitationJournal: J.Am.Chem.Soc. / Year: 2011
Title: The nature of transient dark States in a photoactivatable fluorescent protein.
Authors: Roy, A. / Field, M.J. / Adam, V. / Bourgeois, D.
History
DepositionAug 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2011Group: Structure summary
Revision 1.2Nov 30, 2011Group: Database references
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 / struct_conn / 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 / _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_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

Downloads & links

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Assembly

Deposited unit
A: Green to red photoconvertible GPF-like protein EosFP
B: Green to red photoconvertible GPF-like protein EosFP
C: Green to red photoconvertible GPF-like protein EosFP
D: Green to red photoconvertible GPF-like protein EosFP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,31427
Polymers106,1684
Non-polymers2,14523
Water16,015889
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12890 Å2
ΔGint-236 kcal/mol
Surface area32860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.840, 96.510, 140.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Green to red photoconvertible GPF-like protein EosFP


Mass: 26542.023 Da / Num. of mol.: 4 / Mutation: F173S, F191L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lobophyllia hemprichii (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: Q5S6Z9
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 889 / 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: 2.7 Å3/Da / Density % sol: 54.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: Ammonium sulfate, bicine, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 11, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→79.5 Å / Num. obs: 74096

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→12.984 Å / SU ML: 0.41 / σ(F): 1.77 / Phase error: 19.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1949 3698 4.99 %RANDOM
Rwork0.1566 ---
obs0.1585 74096 95.09 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.849 Å2 / ksol: 0.391 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-13.6584 Å2-0 Å2-0 Å2
2---7.2553 Å20 Å2
3----6.4031 Å2
Refinement stepCycle: LAST / Resolution: 2→12.984 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7134 0 111 889 8134
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067474
X-RAY DIFFRACTIONf_angle_d1.22410095
X-RAY DIFFRACTIONf_dihedral_angle_d14.6382737
X-RAY DIFFRACTIONf_chiral_restr0.0791025
X-RAY DIFFRACTIONf_plane_restr0.0041297
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02620.2651420.19822605X-RAY DIFFRACTION93
2.0262-2.05390.24141360.18872727X-RAY DIFFRACTION96
2.0539-2.08310.21031360.18142674X-RAY DIFFRACTION96
2.0831-2.11410.24311570.16722709X-RAY DIFFRACTION96
2.1141-2.1470.21511340.16142696X-RAY DIFFRACTION96
2.147-2.1820.20881470.15462730X-RAY DIFFRACTION96
2.182-2.21940.21881430.1642713X-RAY DIFFRACTION96
2.2194-2.25960.22991330.17492670X-RAY DIFFRACTION95
2.2596-2.30280.21921500.1672719X-RAY DIFFRACTION96
2.3028-2.34960.21181320.16632725X-RAY DIFFRACTION97
2.3496-2.40030.20881510.16572721X-RAY DIFFRACTION97
2.4003-2.45580.24191370.17272722X-RAY DIFFRACTION96
2.4558-2.51680.24441450.16672698X-RAY DIFFRACTION96
2.5168-2.58430.18611330.17322760X-RAY DIFFRACTION96
2.5843-2.65970.20081480.15762713X-RAY DIFFRACTION96
2.6597-2.74480.23131490.15882726X-RAY DIFFRACTION96
2.7448-2.84190.20231380.16852718X-RAY DIFFRACTION95
2.8419-2.95440.21281440.17132711X-RAY DIFFRACTION96
2.9544-3.08720.22891460.17692721X-RAY DIFFRACTION95
3.0872-3.24750.2381410.16772704X-RAY DIFFRACTION95
3.2475-3.44740.17141410.15932698X-RAY DIFFRACTION94
3.4474-3.70790.16031480.1412706X-RAY DIFFRACTION94
3.7079-4.07050.17131380.12952707X-RAY DIFFRACTION94
4.0705-4.63590.1421440.1152699X-RAY DIFFRACTION94
4.6359-5.75490.14881420.13272708X-RAY DIFFRACTION92
5.7549-12.98420.16991430.17492718X-RAY DIFFRACTION90

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