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- PDB-5oxa: Structure of the S205A mutant of the Cyan Fluorescent Protein Cer... -

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Basic information

Entry
Database: PDB / ID: 5oxa
TitleStructure of the S205A mutant of the Cyan Fluorescent Protein Cerulean at pH 7.0
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / SCFP3A / chromophore / fluorescence
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: 1.16 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 1.4Oct 16, 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


Theoretical massNumber of molelcules
Total (without water)26,7751
Polymers26,7751
Non-polymers00
Water6,990388
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-3 kcal/mol
Surface area10320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.960, 63.320, 69.330
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: 26775.252 Da / Num. of mol.: 1 / Mutation: F64L, S65T, Y66W, N146I, H148D, M153T, S205A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P42212
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 2.2 Å3/Da / Density % sol: 44.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100mM HEPES buffer pH 7.0, 12% PEG8000, 100mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.977178 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 6, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977178 Å / Relative weight: 1
ReflectionResolution: 1.16→46.76 Å / Num. obs: 78153 / % possible obs: 99.9 % / Redundancy: 7.06 % / Rrim(I) all: 0.036 / Net I/σ(I): 24.64
Reflection shellResolution: 1.16→1.19 Å / Redundancy: 6.35 % / Mean I/σ(I) obs: 2.12 / Num. unique obs: 5697 / Rrim(I) all: 0.885 / % possible all: 99.8

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Processing

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

2wso


Resolution: 1.16→46.75 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.983 / SU B: 1.248 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.03 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13856 3894 5 %RANDOM
Rwork0.11569 ---
obs0.11688 74259 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.356 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å2-0 Å2-0 Å2
2---0.73 Å20 Å2
3---1.55 Å2
Refinement stepCycle: 1 / Resolution: 1.16→46.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1791 0 0 388 2179
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192184
X-RAY DIFFRACTIONr_bond_other_d0.0020.021979
X-RAY DIFFRACTIONr_angle_refined_deg1.6891.9843023
X-RAY DIFFRACTIONr_angle_other_deg1.2093.0014643
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6835307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85625.636110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.25915380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.455157
X-RAY DIFFRACTIONr_chiral_restr0.1020.2333
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022536
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02436
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_it1.3151.4411043
X-RAY DIFFRACTIONr_mcbond_other1.3211.4441044
X-RAY DIFFRACTIONr_mcangle_it1.7472.1741326
X-RAY DIFFRACTIONr_mcangle_other1.7322.1741326
X-RAY DIFFRACTIONr_scbond_it1.8951.6521141
X-RAY DIFFRACTIONr_scbond_other1.8941.6531142
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3592.3951667
X-RAY DIFFRACTIONr_long_range_B_refined4.35619.0682403
X-RAY DIFFRACTIONr_long_range_B_other3.46917.6192308
X-RAY DIFFRACTIONr_rigid_bond_restr1.69434163
X-RAY DIFFRACTIONr_sphericity_free34.0075262
X-RAY DIFFRACTIONr_sphericity_bonded9.57454219
LS refinement shellResolution: 1.16→1.19 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 259 -
Rwork0.245 5436 -
obs--99.75 %

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