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- PDB-2wsn: Structure of Enhanced Cyan Fluorescent Protein at physiological pH -

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Basic information

Entry
Database: PDB / ID: 2wsn
TitleStructure of Enhanced Cyan Fluorescent Protein at physiological pH
ComponentsGREEN FLUORESCENT PROTEIN
KeywordsFLUORESCENT PROTEIN / CHROMOPHORE / LUMINESCENCE / PHOTOPROTEIN
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
Green fluorescent protein
Similarity search - Component
Biological speciesAEQUOREA VICTORIA (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsLelimousin, M. / Noirclerc-Savoye, M. / Lazareno-Saez, C. / Paetzold, B. / Le Vot, S. / Chazal, R. / Macheboeuf, P. / Field, M.J. / Bourgeois, D. / Royant, A.
Citation
Journal: Biochemistry / Year: 2009
Title: Intrinsic Dynamics in Ecfp and Cerulean Control Fluorescence Quantum Yield.
Authors: Lelimousin, M. / Noirclerc-Savoye, M. / Lazareno-Saez, C. / Paetzold, B. / Le Vot, S. / Chazal, R. / Macheboeuf, P. / Field, M.J. / Bourgeois, D. / Royant, A.
#1: Journal: J.Mol.Biol. / Year: 2003
Title: Expansion of the Genetic Code Enables Design of a Novel "Gold" Class of Green Fluorescent Proteins.
Authors: Bae, J.H. / Rubini, M. / Jung, G. / Wiegand, G. / Seifert, M.H.J. / Azim, M.K. / Kim, J.S. / Zumbusch, A. / Holak, T.A. / Moroder, L. / Huber, R. / Budisa, N.
History
DepositionSep 8, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 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 1.4Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GREEN FLUORESCENT PROTEIN


Theoretical massNumber of molelcules
Total (without water)26,9201
Polymers26,9201
Non-polymers00
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.182, 62.720, 70.593
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 FLUORESCENT PROTEIN /


Mass: 26920.393 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-238
Source method: isolated from a genetically manipulated source
Details: CHROMOPHORE RESULTING FROM AUTOCATALYTIC CYCLIZATION OF CONSECUTIVE AMINO ACID RESIDUES THR65, TRP66 AND GLY67.
Source: (gene. exp.) AEQUOREA VICTORIA (jellyfish) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 CODONPLUS(DE3) RIL / References: UniProt: P42212
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsGFP VARIANT

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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 Å3/Da / Density % sol: 40 % / Description: NONE
Crystal growpH: 7.5 / Details: 19.5% PEG8000, 4% GLYCEROL, 1M HEPES PH 7.5

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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: Jun 13, 2005 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.37→40 Å / Num. obs: 45997 / % possible obs: 94.9 % / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.3
Reflection shellResolution: 1.37→1.42 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.3 / % possible all: 70.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OXE

1oxe


Resolution: 1.37→35.29 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.976 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.18514 2317 5 %RANDOM
Rwork0.14023 ---
obs0.14248 43679 94.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20 Å2
2--0.09 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.37→35.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1776 0 0 224 2000
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222019
X-RAY DIFFRACTIONr_bond_other_d0.0020.021341
X-RAY DIFFRACTIONr_angle_refined_deg1.8531.9852780
X-RAY DIFFRACTIONr_angle_other_deg0.9593.0013313
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7855274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.42325.40898
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.15115350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.891156
X-RAY DIFFRACTIONr_chiral_restr0.1210.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022313
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02401
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_it1.8721.51211
X-RAY DIFFRACTIONr_mcbond_other0.6781.5490
X-RAY DIFFRACTIONr_mcangle_it2.70621992
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.1963808
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.8444.5768
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.68433360
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.37→1.406 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 117 -
Rwork0.207 2306 -
obs--68.56 %

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