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- PDB-5ox9: Structure of the Cyan Fluorescent Protein SCFP3A at pH 4.5 -

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Basic information

Entry
Database: PDB / ID: 5ox9
TitleStructure of the Cyan Fluorescent Protein SCFP3A at pH 4.5
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / tryptophan-based chromophore / SCFP3A
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: 1.56 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7182
Polymers27,6821
Non-polymers351
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-8 kcal/mol
Surface area10630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.875, 60.396, 69.295
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: 27682.203 Da / Num. of mol.: 1
Mutation: F64L, S65T, Y66W, S72A, N146I, H148D, M153T, V163A, S175G
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.: 156 / 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: 2.15 Å3/Da / Density % sol: 42.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 100mM citric acid pH4.5, 16% PEG8000, 100mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.56→45.53 Å / Num. obs: 31581 / % possible obs: 99.7 % / Redundancy: 3.5 % / Rrim(I) all: 0.067 / Net I/σ(I): 12.2
Reflection shellResolution: 1.56→1.6 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2 / Num. unique obs: 3106 / Rrim(I) all: 0.773 / % possible all: 99.9

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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: 1.56→45.53 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 3.267 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.072 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17233 1583 5 %RANDOM
Rwork0.14313 ---
obs0.14462 29945 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.613 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å2-0 Å2
2---0.14 Å20 Å2
3----0.07 Å2
Refinement stepCycle: 1 / Resolution: 1.56→45.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1800 0 1 156 1957
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191952
X-RAY DIFFRACTIONr_bond_other_d0.0020.021778
X-RAY DIFFRACTIONr_angle_refined_deg1.3491.9832665
X-RAY DIFFRACTIONr_angle_other_deg0.8483.0014144
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1825244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.5725.26395
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.04515337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.108157
X-RAY DIFFRACTIONr_chiral_restr0.0770.2294
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022184
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02384
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_it1.2182.027938
X-RAY DIFFRACTIONr_mcbond_other1.2042.023937
X-RAY DIFFRACTIONr_mcangle_it1.5533.0451178
X-RAY DIFFRACTIONr_mcangle_other1.5563.0471179
X-RAY DIFFRACTIONr_scbond_it1.8092.3371014
X-RAY DIFFRACTIONr_scbond_other1.8112.3391015
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0293.371480
X-RAY DIFFRACTIONr_long_range_B_refined3.08324.2252028
X-RAY DIFFRACTIONr_long_range_B_other2.74223.6461993
X-RAY DIFFRACTIONr_rigid_bond_restr1.01233730
X-RAY DIFFRACTIONr_sphericity_free25.9415100
X-RAY DIFFRACTIONr_sphericity_bonded6.49553731
LS refinement shellResolution: 1.56→1.6 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 121 -
Rwork0.246 2180 -
obs--99.87 %

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