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- PDB-5oxc: Structure of Cerulean Fluorescent Protein at 1.02 Angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 5oxc
TitleStructure of Cerulean Fluorescent Protein at 1.02 Angstrom resolution
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / tryptophan-based chromophore / Cerulean / hydrogen atoms
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: 1.02 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 1.3Jun 20, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.gene_src_common_name ..._entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Jan 17, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Oct 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)26,7911
Polymers26,7911
Non-polymers00
Water7,566420
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-2 kcal/mol
Surface area10380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.010, 62.800, 69.920
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: 26791.252 Da / Num. of mol.: 1 / Mutation: F64L, S65T, Y66W, N146I, H148D, M153T
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.: 420 / 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: 2.19 Å3/Da / Density % sol: 43.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100mM HEPES 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: 0.97934 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 2, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.02→46.73 Å / Num. obs: 114476 / % possible obs: 99.8 % / Redundancy: 6.03 % / Rrim(I) all: 0.05 / Net I/σ(I): 19.51
Reflection shellResolution: 1.02→1.05 Å / Redundancy: 5.46 % / Mean I/σ(I) obs: 2.06 / Num. unique obs: 8333 / Rrim(I) all: 0.838 / % possible all: 99.5

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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: 1.02→46.72 Å / Cor.coef. Fo:Fc: 0.988 / Cor.coef. Fo:Fc free: 0.986 / SU B: 0.578 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.018 / ESU R Free: 0.019 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.11466 5687 5 %RANDOM
Rwork0.09893 ---
obs0.09972 108788 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.437 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å2-0 Å2-0 Å2
2---0.06 Å20 Å2
3---0.31 Å2
Refinement stepCycle: 1 / Resolution: 1.02→46.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1810 0 0 420 2230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.022342
X-RAY DIFFRACTIONr_bond_other_d0.0060.022167
X-RAY DIFFRACTIONr_angle_refined_deg2.2451.9923264
X-RAY DIFFRACTIONr_angle_other_deg1.9793.0025028
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1645344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.11425.833120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.97515432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.329159
X-RAY DIFFRACTIONr_chiral_restr0.1320.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022783
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02519
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_it2.9031.2351105
X-RAY DIFFRACTIONr_mcbond_other2.881.2211099
X-RAY DIFFRACTIONr_mcangle_it3.511.8621420
X-RAY DIFFRACTIONr_mcangle_other3.4731.8471415
X-RAY DIFFRACTIONr_scbond_it3.9191.4411237
X-RAY DIFFRACTIONr_scbond_other3.9171.441238
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3362.0791800
X-RAY DIFFRACTIONr_long_range_B_refined7.34317.0392648
X-RAY DIFFRACTIONr_long_range_B_other7.26916.9642646
X-RAY DIFFRACTIONr_rigid_bond_restr4.25534509
X-RAY DIFFRACTIONr_sphericity_free39.5915224
X-RAY DIFFRACTIONr_sphericity_bonded17.65454607
LS refinement shellResolution: 1.02→1.046 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 390 -
Rwork0.243 7933 -
obs--99.51 %

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