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- PDB-6jgi: Crystal structure of the S65T/F99S/M153T/V163A variant of GFP at ... -

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Basic information

Entry
Database: PDB / ID: 6jgi
TitleCrystal structure of the S65T/F99S/M153T/V163A variant of GFP at 0.85 A
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / Green Fluorescent Protein / hydrogen
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: 0.85 Å
AuthorsTai, Y. / Takaba, K. / Hanazono, Y. / Miki, K. / Takeda, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science17H03643 Japan
CitationJournal: Iucrj / Year: 2019
Title: Subatomic resolution X-ray structures of green fluorescent protein.
Authors: Takaba, K. / Tai, Y. / Eki, H. / Dao, H.A. / Hanazono, Y. / Hasegawa, K. / Miki, K. / Takeda, K.
History
DepositionFeb 14, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: pdbx_related_exp_data_set
Revision 1.2May 29, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)25,8581
Polymers25,8581
Non-polymers00
Water12,052669
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10410 Å2
Unit cell
Length a, b, c (Å)50.857, 62.403, 69.172
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Green fluorescent protein


Mass: 25857.982 Da / Num. of mol.: 1 / Mutation: S65T, F99S, M153T, V163A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P42212
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 669 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence details(1) Residue SER 65 has been mutated to THR 65. Residues THR 65, TYR 66 and GLY 67 constitute the ...(1) Residue SER 65 has been mutated to THR 65. Residues THR 65, TYR 66 and GLY 67 constitute the chromophore CRO 66. The authors state that there are some difference in the structures between CRO in database and CRO in this model. They are in the terminal carboxylic and amino groups and the protonation of phenolic oxygen. (2) Q80R was caused by a PCR error in the early study (Chalfie, M. et al., Science, 1994).

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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: 2.12 Å3/Da / Density % sol: 42.05 %
Crystal growTemperature: 308 K / Method: vapor diffusion / pH: 8.5 / Details: PEG 4000, MgCl2, Tris-HCl buffer

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Data collection

DiffractionMean temperature: 56 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.75 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.75 Å / Relative weight: 1
ReflectionResolution: 0.8→50 Å / Num. obs: 226086 / % possible obs: 97.8 % / Redundancy: 5.7 % / Biso Wilson estimate: 6.36 Å2 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.039 / Rrim(I) all: 0.099 / Χ2: 1.042 / Net I/σ(I): 7.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
0.8-0.815.21.661111370.2950.7911.8470.93697.5
0.81-0.835.41.532112190.3330.721.6980.96297.8
0.83-0.845.31.37111820.3910.6431.5180.99897.9
0.84-0.865.31.18112690.4480.5551.3091.00998
0.86-0.885.30.981112080.5740.4611.0881.02198.1
0.88-0.95.30.817111710.660.3820.9051.05597.7
0.9-0.925.30.666112000.7490.310.7371.0497.1
0.92-0.955.30.53110820.8380.2450.5861.06696.9
0.95-0.985.40.433110920.8930.1990.4791.07496.2
0.98-1.015.50.345109990.9270.1580.3811.06795.9
1.01-1.045.50.268109950.9550.1220.2961.04795.6
1.04-1.095.60.207110120.9710.0930.2281.0795.7
1.09-1.145.70.165112080.9790.0730.1811.12397.1
1.14-1.25.80.14113620.9840.0620.1541.07398.5
1.2-1.275.90.121115100.9870.0530.1321.0499.6
1.27-1.376.10.107115700.990.0470.1171.0699.8
1.37-1.516.30.092116120.9930.040.1011.099100
1.51-1.726.60.076116670.9940.0320.0830.994100
1.72-2.176.80.066117630.9960.0270.0711.068100
2.17-506.50.062118280.9940.0260.0671.01597.4

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WUR

2wur


Resolution: 0.85→46.334 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 11.41
RfactorNum. reflection% reflectionSelection details
Rfree0.1118 9368 4.96 %random selection
Rwork0.0922 ---
obs0.0932 188951 97.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 80.16 Å2 / Biso mean: 10.7096 Å2 / Biso min: 4.13 Å2
Refinement stepCycle: final / Resolution: 0.85→46.334 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1824 0 0 1023 2847
Biso mean---20.09 -
Num. residues----228
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
0.85-0.85970.28233180.26455914623298
0.8597-0.86980.28593120.25045976628898
0.8698-0.88040.26052980.23995901619998
0.8804-0.89150.25773360.22615922625897
0.8915-0.90330.21153240.2165937626198
0.9033-0.91560.21143460.20415833617997
0.9156-0.92870.20322820.18955869615197
0.9287-0.94260.1913040.17595900620497
0.9426-0.95730.1963110.16485873618497
0.9573-0.9730.16553090.15115828613796
0.973-0.98980.1562730.14615862613596
0.9898-1.00780.14252770.13165823610096
1.0078-1.02720.12332980.11955835613396
1.0272-1.04810.11533090.10785796610596
1.0481-1.07090.11012710.09965870614196
1.0709-1.09580.10123260.09315857618396
1.0958-1.12330.09563020.08375896619897
1.1233-1.15360.09912900.08076019630998
1.1536-1.18760.09313180.07765971628999
1.1876-1.22590.09413280.07556064639299
1.2259-1.26970.09523340.073560936427100
1.2697-1.32060.08773110.069661286439100
1.3206-1.38070.09053160.069261246440100
1.3807-1.45350.08353280.067761436471100
1.4535-1.54450.09183350.063861006435100
1.5445-1.66380.09523270.06261726499100
1.6638-1.83120.09053410.064261776518100
1.8312-2.09620.09463030.066562316534100
2.0962-2.6410.08533150.072462676582100
2.641-46.40340.11663260.09616202652895

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