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- PDB-5ox8: Structure of Enhanced Cyan Fluorescent Protein at pH 5.0 -

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Basic information

Entry
Database: PDB / ID: 5ox8
TitleStructure of Enhanced Cyan Fluorescent Protein at pH 5.0
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / tryptophan-based chromophore / ECFP
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: 1.29 Å
AuthorsGotthard, G. / von Stetten, D. / Clavel, D. / Noirclerc-Savoye, M. / Royant, A.
CitationJournal: Biochemistry / Year: 2017
Title: Chromophore Isomer Stabilization Is Critical to the Efficient Fluorescence of Cyan Fluorescent Proteins.
Authors: Gotthard, G. / von Stetten, D. / Clavel, D. / Noirclerc-Savoye, M. / Royant, A.
History
DepositionSep 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / Item: _citation.journal_id_ISSN / _citation.title
Revision 1.2Dec 20, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9582
Polymers26,9221
Non-polymers351
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-10 kcal/mol
Surface area10100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.247, 62.624, 69.108
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: 26922.408 Da / Num. of mol.: 1 / Mutation: F64L, S65T, Y66W, N146I, M153T
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) / Gene: GFP / Plasmid: pQE-60 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P42212
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.21 Å3/Da / Density % sol: 44.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 100mM citric acid pH 5.0, 12% PEG8000, 100mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07166 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 8, 2012
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07166 Å / Relative weight: 1
ReflectionResolution: 1.29→46.4 Å / Num. obs: 55928 / % possible obs: 98.9 % / Redundancy: 4.4 % / Rrim(I) all: 0.036 / Net I/σ(I): 18.8
Reflection shellResolution: 1.29→1.36 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2 / Num. unique obs: 5470 / Rrim(I) all: 0.88 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WSO

2wso


Resolution: 1.29→39.66 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.933 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.046 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1664 2841 5.1 %RANDOM
Rwork0.13221 ---
obs0.13395 53030 98.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.928 Å2
Baniso -1Baniso -2Baniso -3
1-1.58 Å20 Å20 Å2
2---0.57 Å20 Å2
3----1.01 Å2
Refinement stepCycle: 1 / Resolution: 1.29→39.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1792 0 1 296 2089
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192155
X-RAY DIFFRACTIONr_bond_other_d0.0020.021947
X-RAY DIFFRACTIONr_angle_refined_deg1.7121.9782979
X-RAY DIFFRACTIONr_angle_other_deg0.9723.0014566
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6045299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.5425.413109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.59515380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.701158
X-RAY DIFFRACTIONr_chiral_restr0.0960.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022496
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02433
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_it1.5781.881024
X-RAY DIFFRACTIONr_mcbond_other1.4761.8771023
X-RAY DIFFRACTIONr_mcangle_it1.9582.8351306
X-RAY DIFFRACTIONr_mcangle_other1.9652.8381307
X-RAY DIFFRACTIONr_scbond_it2.3762.1921131
X-RAY DIFFRACTIONr_scbond_other2.3752.1941132
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8383.1741648
X-RAY DIFFRACTIONr_long_range_B_refined5.2524.8892406
X-RAY DIFFRACTIONr_long_range_B_other4.07823.5922330
X-RAY DIFFRACTIONr_rigid_bond_restr2.16834102
X-RAY DIFFRACTIONr_sphericity_free36.1925181
X-RAY DIFFRACTIONr_sphericity_bonded15.10854143
LS refinement shellResolution: 1.29→1.323 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 231 -
Rwork0.272 3806 -
obs--97.61 %

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