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- PDB-6jgj: Crystal structure of the F99S/M153T/V163A/E222Q variant of GFP at... -

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Basic information

Entry
Database: PDB / ID: 6jgj
TitleCrystal structure of the F99S/M153T/V163A/E222Q variant of GFP at 0.78 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: 0.78 Å
AuthorsTakaba, K. / Tai, Y. / 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_symmetry
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)25,8923
Polymers25,8431
Non-polymers492
Water11,458636
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40 Å2
ΔGint-2 kcal/mol
Surface area10380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.870, 62.340, 68.850
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: 25842.973 Da / Num. of mol.: 1 / Mutation: E222Q, 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 636 / Source method: isolated from a natural source / Formula: H2O
Compound detailsThe authors state that there are some difference in the structures between CRO in database and CRO ...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.
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: 2.11 Å3/Da / Density % sol: 41.73 %
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: BL41XU / Wavelength: 0.35 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.35 Å / Relative weight: 1
ReflectionResolution: 0.77→31.14 Å / Num. obs: 254665 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 11.873 % / Biso Wilson estimate: 8.04 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rrim(I) all: 0.076 / Χ2: 0.949 / Net I/σ(I): 15.68
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
0.78-0.88.632.0981.12227210.5072.22998
0.8-0.8111.031.711.56183730.6531.79399.8
0.81-0.8411.2821.3731.98179190.7341.43899.9
0.84-0.8611.4221.1532.35173750.791.20799.9
0.86-0.8911.5520.8883.09168940.8610.928100
0.89-0.9211.7020.6734.07163430.9090.704100
0.92-0.9611.860.4985.49157630.9490.52100
0.96-0.9912.0420.3677.3151910.9710.383100
0.99-1.0412.2230.2759.66145690.9850.287100
1.04-1.0912.4710.18513.71139330.9930.19399.9
1.09-1.1512.6720.12918.99133250.9960.135100
1.15-1.2212.9850.10622.64125880.9980.11100
1.22-1.312.9580.09425.01118220.9980.098100
1.3-1.4112.9640.08228.35110550.9980.08699.9
1.41-1.5413.4110.06434.67100220.9990.06798.4
1.54-1.7213.2530.04942.8489310.9990.05196.5
1.72-1.9911.2980.0447.7377600.9990.04294.5
1.99-2.4310.890.03656.4663820.9990.03791.4
2.43-3.4414.4150.03570.6754730.9990.037100
3.44-31.1413.0710.03971.7831270.9980.0499.7

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Processing

Software
NameVersionClassification
SHELXLrefinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WUR

2wur


Resolution: 0.78→31.14 Å / Cross valid method: FREE R-VALUE
Details: This model was finally refined with Multipolar Atomic Model using MoPro program but the determined multipolar parameters are not included.
RfactorNum. reflection% reflectionSelection details
Rfree0.125 12719 4.99 %Random selection
Rwork0.108 ---
obs-254639 99.2 %-
Displacement parametersBiso max: 85.31 Å2 / Biso mean: 11.0321 Å2 / Biso min: 4.57 Å2
Refinement stepCycle: LAST / Resolution: 0.78→31.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1803 0 1 636 2440
LS refinement shellResolution: 0.78→0.8 Å /
Num. reflection% reflection
obs22721 98 %

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