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- PDB-6jgh: Crystal structure of the F99S/M153T/V163A/T203I variant of GFP at... -

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Basic information

Entry
Database: PDB / ID: 6jgh
TitleCrystal structure of the F99S/M153T/V163A/T203I variant of GFP at 0.94 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: 0.94 Å
AuthorsEki, H. / Tai, 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 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _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)25,8912
Polymers25,8561
Non-polymers351
Water9,764542
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-10 kcal/mol
Surface area10400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.641, 62.506, 68.179
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Green fluorescent protein /


Mass: 25856.012 Da / Num. of mol.: 1 / Mutation: T203I, 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: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 542 / Source method: isolated from a natural source / Formula: H2O
Sequence details(1) The mutated chromophore, CRO, was used an initial model for refinement. Its hydroxyethyl group ...(1) The mutated chromophore, CRO, was used an initial model for refinement. Its hydroxyethyl group inserted to the model by S65T mutation was replaced with original hydoxymethyl in the refinement step, and finally its name was changed to GYS. (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: 2.09 Å3/Da / Density % sol: 41.02 %
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: Dec 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.75 Å / Relative weight: 1
ReflectionResolution: 0.94→50 Å / Num. obs: 141942 / % possible obs: 99.8 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.047 / Rrim(I) all: 0.154 / Χ2: 1.048 / Net I/σ(I): 5.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
0.94-0.967.11.2669690.5420.5031.3580.91399.3
0.96-0.977.11.12569850.6040.4481.2130.95499.3
0.97-0.997.10.96368960.660.3841.0380.99799.4
0.99-1.017.20.84470170.7360.3360.91199.4
1.01-1.037.20.74370180.7850.2950.81.03199.5
1.03-1.067.20.63369990.8270.2520.6821.09199.5
1.06-1.097.20.51170420.9030.2030.5511.04399.8
1.09-1.117.20.41770290.9120.1660.4491.11199.9
1.11-1.157.20.36570770.9370.1450.3931.17299.9
1.15-1.187.20.31170720.9590.1230.3351.11299.9
1.18-1.237.20.28770470.9630.1140.3091.085100
1.23-1.287.20.26471070.9660.1050.2851.129100
1.28-1.337.30.2470740.9720.0950.2591.114100
1.33-1.47.30.22471250.9750.0890.2411.143100
1.4-1.497.30.18271080.9830.0720.1961.041100
1.49-1.6113.80.371200.9890.0820.3121.044100
1.61-1.7714.70.23471600.9920.0630.2431.012100
1.77-2.0314.50.1572260.9960.0410.1551.021100
2.03-2.5514.50.10472520.9980.0280.1071.017100
2.55-5011.90.06475290.9980.0190.0671.03799.9

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Processing

Software
NameClassification
SHELXLrefinement
HKL-2000data collection
SDMSdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WUR

2wur


Resolution: 0.94→29.928 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 12.25
RfactorNum. reflection% reflectionSelection details
Rfree0.129 13451 4.95 %random selection
Rwork0.1069 ---
obs0.108 140511 99.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 0.94→29.928 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1823 0 1 542 2366
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.94-0.95070.27355000.25198552X-RAY DIFFRACTION100
0.9507-0.96190.24594250.23828536X-RAY DIFFRACTION99
0.9619-0.97360.21844760.22878540X-RAY DIFFRACTION99
0.9736-0.98590.21343930.22398651X-RAY DIFFRACTION100
0.9859-0.99890.23864180.21418575X-RAY DIFFRACTION99
0.9989-1.01260.20544140.19718585X-RAY DIFFRACTION99
1.0126-1.02710.20914740.1918597X-RAY DIFFRACTION100
1.0271-1.04240.18314180.17968595X-RAY DIFFRACTION100
1.0424-1.05870.20164350.1738639X-RAY DIFFRACTION100
1.0587-1.0760.16814520.1568620X-RAY DIFFRACTION100
1.076-1.09460.15134830.14538522X-RAY DIFFRACTION100
1.0946-1.11450.13954440.13328681X-RAY DIFFRACTION100
1.1145-1.13590.1463970.12498643X-RAY DIFFRACTION100
1.1359-1.15910.14274340.11788596X-RAY DIFFRACTION100
1.1591-1.18430.13475020.11188604X-RAY DIFFRACTION100
1.1843-1.21190.14054370.10928604X-RAY DIFFRACTION100
1.2119-1.24220.13134410.10698582X-RAY DIFFRACTION100
1.2422-1.27580.1224760.10368620X-RAY DIFFRACTION100
1.2758-1.31330.1184490.10138618X-RAY DIFFRACTION100
1.3133-1.35570.11374570.09718609X-RAY DIFFRACTION100
1.3557-1.40410.1154360.09618638X-RAY DIFFRACTION100
1.4041-1.46040.11594610.08838610X-RAY DIFFRACTION100
1.4604-1.52680.11514850.08478597X-RAY DIFFRACTION100
1.5268-1.60730.10024550.07718614X-RAY DIFFRACTION100
1.6073-1.7080.1154840.07458558X-RAY DIFFRACTION100
1.708-1.83990.10524760.07318610X-RAY DIFFRACTION100
1.8399-2.0250.10054260.06968665X-RAY DIFFRACTION100
2.025-2.31790.08864190.07128642X-RAY DIFFRACTION100
2.3179-2.91990.09524290.07528634X-RAY DIFFRACTION100
2.9199-29.94310.12034550.09378603X-RAY DIFFRACTION100

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