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- PDB-6j1b: Photoswitchable fluorescent protein Gamillus, N150C/T204V double ... -

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Basic information

Entry
Database: PDB / ID: 6j1b
TitlePhotoswitchable fluorescent protein Gamillus, N150C/T204V double mutant, on-state
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / acid-tolerant / photoswitchable / N150C/T204V double mutant / trans-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 / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsNakashima, R. / 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
DepositionDec 28, 2018Deposition 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)30,6555
Polymers30,3971
Non-polymers2584
Water3,927218
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 area10520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.492, 161.492, 161.492
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: 30397.307 Da / Num. of mol.: 1 / Mutation: N150C, T204V
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 / Phosphate


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 / Glycerol


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsResidues 150CYS and 204VAL represent mutations (N150C/T204V).

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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: 5.77 Å3/Da / Density % sol: 78.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: mmonium phosphate, sodium citrate, sodium chloride, HEPES, pH5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.99→46.619 Å / Num. obs: 47626 / % possible obs: 100 % / Redundancy: 14.402 % / Biso Wilson estimate: 26.014 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rrim(I) all: 0.073 / Χ2: 1.026 / Net I/σ(I): 27.64 / Num. measured all: 685896
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
1.99-2.1213.780.2548.75105459765476530.9860.264100
2.12-2.2614.5730.18113.12104459716871680.9940.188100
2.26-2.4414.6560.13917.3798283670667060.9960.144100
2.44-2.6714.6880.10822.9990490616161610.9980.111100
2.67-2.9914.6430.08230.9681871559155910.9980.085100
2.99-3.4514.4370.06141.571464495049500.9990.063100
3.45-4.2214.2560.04851.8260102421642160.9990.05100
4.22-5.9414.3150.0458.1446923327832780.9990.041100
5.94-46.61914.1070.03257.62268451909190310.03499.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y00

5y00


Resolution: 1.99→46.62 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.39 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1602 2382 5 %RANDOM
Rwork0.1427 ---
obs0.1435 45244 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98.64 Å2 / Biso mean: 22.005 Å2 / Biso min: 10.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.99→46.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1811 0 483 218 2512
Biso mean--21.02 30.19 -
Num. residues----168
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0191876
X-RAY DIFFRACTIONr_bond_other_d0.0020.021744
X-RAY DIFFRACTIONr_angle_refined_deg2.7091.9642540
X-RAY DIFFRACTIONr_angle_other_deg1.21434034
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1965229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.15624.2580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.13615309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.563157
X-RAY DIFFRACTIONr_chiral_restr0.1690.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0212093
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02430
LS refinement shellResolution: 1.995→2.047 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 176 -
Rwork0.195 3330 -
all-3506 -
obs--100 %

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