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- PDB-6jxf: Photoswitchable fluorescent protein Gamillus, off-state (pH7.0) -

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Basic information

Entry
Database: PDB / ID: 6jxf
TitlePhotoswitchable fluorescent protein Gamillus, off-state (pH7.0)
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / acid-tolerant / photoswitchable / cis-chromophore
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
PHOSPHATE ION / Green fluorescent protein
Similarity search - Component
Biological speciesOlindias (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNakashima, R. / Sakurai, K. / shinoda, H. / Matsuda, T. / Nagai, T.
CitationJournal: Cell Chem Biol / Year: 2019
Title: Acid-Tolerant Reversibly Switchable Green Fluorescent Protein for Super-resolution Imaging under Acidic Conditions.
Authors: Shinoda, H. / Lu, K. / Nakashima, R. / Wazawa, T. / Noguchi, K. / Matsuda, T. / Nagai, T.
History
DepositionApr 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr2_label_atom_id
Revision 2.1Nov 22, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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)30,7046
Polymers30,4101
Non-polymers2935
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-11 kcal/mol
Surface area10430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.711, 161.711, 161.711
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213

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Components

#1: Protein Green fluorescent protein


Mass: 30410.236 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Olindias (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2Z5X7U3*PLUS
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O

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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: 5.79 Å3/Da / Density % sol: 78.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Ammonium phosphate, sodium citrate, sodium chloride, HEPES, pH5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.8→46.682 Å / Num. obs: 64910 / % possible obs: 99.7 % / Redundancy: 7.408 % / Biso Wilson estimate: 32.623 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.069 / Χ2: 1.039 / Net I/σ(I): 17.34 / Num. measured all: 480868
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.917.550.4383.917849410452103960.9390.4799.5
1.91-2.047.5790.2576.9474414982598190.9740.27699.9
2.04-2.27.5870.15711.0769579917191710.9890.169100
2.2-2.417.4160.11915.4362607845784420.9930.12899.8
2.41-2.697.4350.08321.0156774763676360.9960.09100
2.69-3.117.3740.06227.5749963677767760.9970.067100
3.11-3.87.1550.05132.9840999573857300.9980.05599.9
3.8-5.367.0360.0436.2631576450144880.9990.04399.7
5.36-46.6826.7140.03535.0616462257824520.9990.03895.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XDSdata scaling
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y00

5y00


Resolution: 1.8→46.68 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.223 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1677 3247 5 %RANDOM
Rwork0.1536 ---
obs0.1543 61681 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.23 Å2 / Biso mean: 29.584 Å2 / Biso min: 17.51 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.8→46.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1813 0 484 218 2515
Biso mean--28.27 39.49 -
Num. residues----168
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0340.0191913
X-RAY DIFFRACTIONr_bond_other_d0.0030.021761
X-RAY DIFFRACTIONr_angle_refined_deg2.9391.9732597
X-RAY DIFFRACTIONr_angle_other_deg1.33734077
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3585233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26624.3982
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.58815313
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.118157
X-RAY DIFFRACTIONr_chiral_restr0.2080.2280
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.0212149
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02442
LS refinement shellResolution: 1.798→1.845 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 236 -
Rwork0.275 4481 -
all-4717 -
obs--99.03 %

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