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- PDB-6vio: Crystal structure of eYFP His148Ser -

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Basic information

Entry
Database: PDB / ID: 6vio
TitleCrystal structure of eYFP His148Ser
ComponentsGreen fluorescent protein GFP
KeywordsFLUORESCENT PROTEIN / yellow / enhanced / modulatable
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / Green fluorescent protein GFP / Green fluorescent protein
Function and homology information
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.6 Å
AuthorsLieberman, R.L. / Hill, S.E. / Patterson-Orazem, A.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)R01EY021205 United States
CitationJournal: J.Phys.Chem.B / Year: 2021
Title: Optically Modulated and Optically Activated Delayed Fluorescent Proteins through Dark State Engineering
Authors: Peng, B. / Dikdan, R. / Hill, S.E. / Patterson-Orazem, A.C. / Lieberman, R.L. / Fahrni, C.J. / Dickson, R.M.
History
DepositionJan 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Green fluorescent protein GFP
B: Green fluorescent protein GFP
C: Green fluorescent protein GFP
D: Green fluorescent protein GFP
E: Green fluorescent protein GFP
F: Green fluorescent protein GFP
G: Green fluorescent protein GFP
H: Green fluorescent protein GFP


Theoretical massNumber of molelcules
Total (without water)235,3298
Polymers235,3298
Non-polymers00
Water00
1
A: Green fluorescent protein GFP


Theoretical massNumber of molelcules
Total (without water)29,4161
Polymers29,4161
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Green fluorescent protein GFP


Theoretical massNumber of molelcules
Total (without water)29,4161
Polymers29,4161
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Green fluorescent protein GFP


Theoretical massNumber of molelcules
Total (without water)29,4161
Polymers29,4161
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Green fluorescent protein GFP


Theoretical massNumber of molelcules
Total (without water)29,4161
Polymers29,4161
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Green fluorescent protein GFP


Theoretical massNumber of molelcules
Total (without water)29,4161
Polymers29,4161
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Green fluorescent protein GFP


Theoretical massNumber of molelcules
Total (without water)29,4161
Polymers29,4161
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Green fluorescent protein GFP


Theoretical massNumber of molelcules
Total (without water)29,4161
Polymers29,4161
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Green fluorescent protein GFP


Theoretical massNumber of molelcules
Total (without water)29,4161
Polymers29,4161
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.651, 56.772, 148.193
Angle α, β, γ (deg.)85.120, 85.260, 70.480
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 6 through 230)
21(chain B and resid 6 through 230)
31(chain C and resid 6 through 230)
41(chain D and resid 6 through 230)
51(chain E and resid 6 through 230)
61(chain F and resid 6 through 230)
71(chain G and resid 6 through 230)
81(chain H and resid 6 through 230)

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: THR / End label comp-ID: THR / Auth seq-ID: 6 - 230 / Label seq-ID: 30 - 252

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain A and resid 6 through 230)AA
2(chain B and resid 6 through 230)BB
3(chain C and resid 6 through 230)CC
4(chain D and resid 6 through 230)DD
5(chain E and resid 6 through 230)EE
6(chain F and resid 6 through 230)FF
7(chain G and resid 6 through 230)GG
8(chain H and resid 6 through 230)HH

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Components

#1: Protein
Green fluorescent protein GFP


Mass: 29416.145 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5J6CYR6, UniProt: P42212*PLUS
Has ligand of interestY

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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

CrystalDescription: plate
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1.75 M Na/K phosphate pH 6.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 18449 / % possible obs: 91.4 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.128 / Rrim(I) all: 0.207 / Χ2: 1.329 / Net I/σ(I): 4.4 / Num. measured all: 40830
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.6-3.662.40.8539440.7630.6221.0620.60997.9
3.66-3.732.40.7510040.7410.5560.9390.77796.4
3.73-3.82.40.6710390.7860.4910.8360.73397.8
3.8-3.882.30.5239220.840.3930.6580.76496.4
3.88-3.962.30.56810060.8230.4260.7140.89496.5
3.96-4.052.40.3779560.9060.2810.4730.9496.7
4.05-4.162.30.3429370.9160.2590.4321.23394.8
4.16-4.272.30.2929710.9410.230.3741.21995.1
4.27-4.392.20.2529760.9450.1940.321.23293.1
4.39-4.542.20.2128880.960.1740.2761.52591.7
4.54-4.72.10.1849040.9640.150.2381.27789.9
4.7-4.892.10.1729250.9650.140.2231.39490.7
4.89-5.112.10.1488820.9780.1210.1921.45687.2
5.11-5.3820.1378680.9850.1140.1791.51287
5.38-5.711.90.1479000.9780.1220.1931.49186.5
5.71-6.1520.1548700.9680.1240.1991.6986.6
6.15-6.772.30.1168960.9920.0890.1471.65290.5
6.77-7.752.30.0878920.9910.070.1131.7788.8
7.75-9.752.20.0718530.990.0620.0952.72383.5
9.75-502.10.0568160.9920.050.0753.05881

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.51 Å41.01 Å
Translation3.51 Å41.01 Å

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHASER2.8.2phasing
PHENIX1.15.2refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V3D

3v3d


Resolution: 3.6→37.38 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 40.23
RfactorNum. reflection% reflection
Rfree0.3101 1744 9.91 %
Rwork0.2372 --
obs0.245 17595 87.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 178.93 Å2 / Biso mean: 104.1115 Å2 / Biso min: 66.38 Å2
Refinement stepCycle: final / Resolution: 3.6→37.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14010 0 0 0 14010
Num. residues----1809
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5360X-RAY DIFFRACTION0.921TORSIONAL
12B5360X-RAY DIFFRACTION0.921TORSIONAL
13C5360X-RAY DIFFRACTION0.921TORSIONAL
14D5360X-RAY DIFFRACTION0.921TORSIONAL
15E5360X-RAY DIFFRACTION0.921TORSIONAL
16F5360X-RAY DIFFRACTION0.921TORSIONAL
17G5360X-RAY DIFFRACTION0.921TORSIONAL
18H5360X-RAY DIFFRACTION0.921TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.6001-3.7060.34091350.342122982
3.706-3.82550.3931660.3252145796
3.8255-3.96210.34451520.2928143096
3.9621-4.12050.28551570.248142895
4.1205-4.30780.35071580.2533139993
4.3078-4.53460.26651490.2371134090
4.5346-4.81810.28781480.222135289
4.8181-5.18920.29271360.2204127684
5.1892-5.70980.27641400.2324125982
5.7098-6.53220.34181340.2535125185
6.5322-8.21550.29921430.238134189
8.2155-37.380.3081260.1689108973

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