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- PDB-6j1c: Photoswitchable fluorescent protein Gamillus, N150C/T204V double ... -

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Basic information

Entry
Database: PDB / ID: 6j1c
TitlePhotoswitchable fluorescent protein Gamillus, N150C/T204V double mutant, off-state
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / acid-tolerant / photoswitchable / N150C/T204V double mutant / 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
Green fluorescent protein
Similarity search - Component
Biological speciesOlindias (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.09 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 1.1Mar 25, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
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)30,5965
Polymers30,3971
Non-polymers1984
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-12 kcal/mol
Surface area10550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.021, 162.021, 162.021
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-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 165 / 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: 5.83 Å3/Da / Density % sol: 78.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Ammonium 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 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.09→46.772 Å / Num. obs: 41594 / % possible obs: 99.9 % / Redundancy: 7.34 % / Biso Wilson estimate: 37.341 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rrim(I) all: 0.076 / Χ2: 1.084 / Net I/σ(I): 19.44 / Num. measured all: 305306
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
2.09-2.227.2710.5113.5448459667866650.9090.55199.8
2.22-2.377.350.3425.345905623862460.960.368100
2.37-2.567.3880.2178.2743226585158510.9840.233100
2.56-2.817.4210.13313.5139994539053890.9930.143100
2.81-3.147.4320.08520.8336253487948780.9970.091100
3.14-3.627.3640.05532.3631991434443440.9980.059100
3.62-4.437.2610.04143.1826727368236810.9990.044100
4.43-6.237.2980.03350.0621019288028800.9990.036100
6.23-46.7727.0670.02851.4611732167616600.9990.0399

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y00

5y00


Resolution: 2.09→46.77 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.058 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1769 2080 5 %RANDOM
Rwork0.1613 ---
obs0.162 39511 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.47 Å2 / Biso mean: 31.497 Å2 / Biso min: 20.65 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.09→46.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1811 0 479 165 2455
Biso mean--32.42 40.99 -
Num. residues----168
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0131872
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171690
X-RAY DIFFRACTIONr_angle_refined_deg2.2531.6722536
X-RAY DIFFRACTIONr_angle_other_deg1.5821.5893942
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8535229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.5223.10387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5415309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.411157
X-RAY DIFFRACTIONr_chiral_restr0.1020.2246
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.022080
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02383
LS refinement shellResolution: 2.094→2.148 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 151 -
Rwork0.225 2872 -
all-3023 -
obs--100 %

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