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- PDB-6kl0: Crystal structure of the S65T/F99S/M153T/V163A variant of perdeut... -

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Basic information

Entry
Database: PDB / ID: 6kl0
TitleCrystal structure of the S65T/F99S/M153T/V163A variant of perdeuterated GFP at pD 7.0
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / Green Fluorescent Protein / visualization of hydrogen / perdeuteration / high resolution
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / DEUTERATED WATER / Green fluorescent protein
Function and homology information
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.798 Å
AuthorsTai, Y. / Takaba, K. / Hanazono, Y. / Miki, K. / Takeda, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science17H03643 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)Photon and Quantum Basic Research Coordinated Development Program Japan
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2019
Title: X-ray crystallographic studies on the hydrogen isotope effects of green fluorescent protein at sub-angstrom resolutions
Authors: Tai, Y. / Takaba, K. / Hanazono, Y. / Dao, H.A. / Miki, K. / Takeda, K.
History
DepositionJul 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 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 1.2Nov 20, 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
Water10,917606
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10260 Å2
Unit cell
Length a, b, c (Å)50.826, 62.402, 68.875
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) / References: UniProt: P42212
#2: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 606 / Source method: isolated from a natural source / Formula: D2O
Has ligand of interestY
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: 2.11 Å3/Da / Density % sol: 41.76 %
Crystal growTemperature: 308 K / Method: vapor diffusion / pH: 6.6 / Details: PEG 4000, MgCl2, Tris-DCl buffer

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Data collection

DiffractionMean temperature: 50 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.75 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.75 Å / Relative weight: 1
ReflectionResolution: 0.798→50 Å / Num. obs: 229145 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 6.16 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 29.6
Reflection shellResolution: 0.798→0.81 Å / Redundancy: 6 % / Rmerge(I) obs: 1.459 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 11357 / CC1/2: 0.475 / % possible all: 99.8
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
DENZOdata reduction
MOLREPphasing
SHELXLrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WUR

2wur


Resolution: 0.798→26.59 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 13.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1198 11370 4.97 %
Rwork0.106 217633 -
obs0.1067 229003 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.15 Å2 / Biso mean: 10.2835 Å2 / Biso min: 3.57 Å2
Refinement stepCycle: final / Resolution: 0.798→26.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1823 0 0 897 2720
Biso mean---25.48 -
Num. residues----228
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
0.7983-0.80740.30982600.3276495268
0.8074-0.81690.3563990.33347205100
0.8169-0.82690.31463690.32247236100
0.8269-0.83730.26833890.2967284100
0.8373-0.84830.26723810.26977292100
0.8483-0.860.26153710.2467270100
0.86-0.87220.23913750.22747275100
0.8722-0.88530.19834010.2067253100
0.8853-0.89910.20233920.1877244100
0.8991-0.91380.18524260.17527247100
0.9138-0.92960.17943530.16067365100
0.9296-0.94650.16093620.14627299100
0.9465-0.96470.16263840.13967231100
0.9647-0.98440.13683750.13037342100
0.9844-1.00580.14133530.1237316100
1.0058-1.02920.12973750.1177326100
1.0292-1.05490.10643610.10287309100
1.0549-1.08350.09233910.09567305100
1.0835-1.11540.0923830.08757332100
1.1154-1.15140.09313590.08157324100
1.1514-1.19250.10124040.0817315100
1.1925-1.24030.09253700.08127371100
1.2403-1.29670.09243930.08087339100
1.2967-1.36510.09343930.07957323100
1.3651-1.45060.08633850.07697401100
1.4506-1.56260.09754010.07597353100
1.5626-1.71980.0954030.07577397100
1.7198-1.96860.09994010.07997434100
1.9686-2.47990.09493620.08287518100
2.4799-26.590.1193990.10077775100

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