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- PDB-3p8u: Crystal structure of mEosFP in its green state -

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Basic information

Entry
Database: PDB / ID: 3p8u
TitleCrystal structure of mEosFP in its green state
ComponentsGreen to red photoconvertible GPF-like protein EosFP
KeywordsFLUORESCENT PROTEIN / Beta-barrel
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: 2.25 Å
AuthorsAdam, V. / Nienhaus, G.U. / Bourgeois, D.
CitationJournal: Chem.Biol. / Year: 2011
Title: Rational design of photoconvertible and biphotochromic fluorescent proteins for advanced microscopy applications.
Authors: Adam, V. / Moeyaert, B. / David, C.C. / Mizuno, H. / Lelimousin, M. / Dedecker, P. / Ando, R. / Miyawaki, A. / Michiels, J. / Engelborghs, Y. / Hofkens, J.
History
DepositionOct 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Database references
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)108,46223
Polymers106,7014
Non-polymers1,76119
Water6,882382
1
A: Green to red photoconvertible GPF-like protein EosFP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2207
Polymers26,6751
Non-polymers5446
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Green to red photoconvertible GPF-like protein EosFP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1396
Polymers26,6751
Non-polymers4645
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Green to red photoconvertible GPF-like protein EosFP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9634
Polymers26,6751
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Green to red photoconvertible GPF-like protein EosFP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1396
Polymers26,6751
Non-polymers4645
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11870 Å2
ΔGint-214.8 kcal/mol
Surface area33470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.450, 96.820, 140.430
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: 26675.150 Da / Num. of mol.: 4 / Mutation: V123T T158H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lobophyllia hemprichii (invertebrata) / Plasmid: pQE32 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5S6Z9
#2: Chemical
ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsHIS 62, TYR 63 AND GLY 64 CIRCULARIZED INTO ONE CHROMOPHORE

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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: 2.75 Å3/Da / Density % sol: 55.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2.2 M ammonium sulfate, 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 16, 2007 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.25→56.796 Å / Num. all: 80225 / Num. obs: 74471 / % possible obs: 92.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.25→2.5 Å / % possible all: 99.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0072refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZUX

1zux


Resolution: 2.25→48.41 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.907 / SU B: 9.796 / SU ML: 0.228 / Cross valid method: THROUGHOUT / ESU R: 0.312 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28352 2817 5 %RANDOM
Rwork0.23175 ---
obs0.23434 53525 100 %-
all-56351 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.273 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.25→48.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7180 0 91 382 7653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0217599
X-RAY DIFFRACTIONr_bond_other_d0.0070.025208
X-RAY DIFFRACTIONr_angle_refined_deg1.421.96810291
X-RAY DIFFRACTIONr_angle_other_deg0.87312660
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0685923
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.05924.096376
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.088151276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8251536
X-RAY DIFFRACTIONr_chiral_restr0.0780.21026
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218475
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021617
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4251.54457
X-RAY DIFFRACTIONr_mcbond_other0.0421.51842
X-RAY DIFFRACTIONr_mcangle_it0.79427189
X-RAY DIFFRACTIONr_scbond_it0.76833142
X-RAY DIFFRACTIONr_scangle_it1.294.53076
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.461 204 -
Rwork0.428 3875 -
obs--100 %

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