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- PDB-7a8h: rsGreen0.7-K206A-H148S in the green-on state -

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Basic information

Entry
Database: PDB / ID: 7a8h
TitlersGreen0.7-K206A-H148S in the green-on state
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / Reversible photoswitchable fluorescent protein
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
Function and homology information
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsDe Zitter, E. / Dedecker, P. / Van Meervelt, L.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders Belgium
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Structure-Function Dataset Reveals Environment Effects within a Fluorescent Protein Model System*.
Authors: De Zitter, E. / Hugelier, S. / Duwe, S. / Vandenberg, W. / Tebo, A.G. / Van Meervelt, L. / Dedecker, P.
History
DepositionAug 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Green fluorescent protein
B: Green fluorescent protein
C: Green fluorescent protein
D: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,3035
Polymers122,2414
Non-polymers621
Water16,087893
1
A: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)30,5601
Polymers30,5601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)30,5601
Polymers30,5601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6222
Polymers30,5601
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)30,5601
Polymers30,5601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.593, 98.601, 100.035
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: 30560.271 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: gfp / Production host: Escherichia coli (E. coli) / Variant (production host): JM109 / References: UniProt: A0A059PIQ0
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 893 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 47.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM Bis-tris pH 6.5 20 % PEG 5000 mme

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 28, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.7→44.51 Å / Num. obs: 106573 / % possible obs: 100 % / Redundancy: 13 % / Biso Wilson estimate: 24.4 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.014 / Rrim(I) all: 0.051 / Net I/σ(I): 27.9 / Num. measured all: 1384862
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.7-1.7313.50.7577081852590.9090.2160.7883.699.9
9.31-44.519.20.03367687380.9990.0120.03661.698.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.98 Å44.51 Å
Translation5.98 Å44.51 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.32data scaling
PHASER2.7.16phasing
PHENIX1.11refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→44.512 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2091 5262 4.94 %
Rwork0.1792 101216 -
obs0.1807 106478 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.21 Å2 / Biso mean: 29.5196 Å2 / Biso min: 12.69 Å2
Refinement stepCycle: final / Resolution: 1.7→44.512 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7199 0 4 893 8096
Biso mean--36.45 38.02 -
Num. residues----911
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077795
X-RAY DIFFRACTIONf_angle_d0.86810616
X-RAY DIFFRACTIONf_chiral_restr0.0631147
X-RAY DIFFRACTIONf_plane_restr0.0051416
X-RAY DIFFRACTIONf_dihedral_angle_d18.2144631
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7-1.71930.31191860.263332893475
1.7193-1.73950.2751780.238433603538
1.7395-1.76080.27181760.235133363512
1.7608-1.7830.28521640.232533523516
1.783-1.80650.351700.271133293499
1.8065-1.83130.30761780.250833253503
1.8313-1.85740.30141590.235233883547
1.8574-1.88510.28761630.224833243487
1.8851-1.91460.29391580.220333633521
1.9146-1.9460.27031650.211233593524
1.946-1.97960.29371910.198433363527
1.9796-2.01550.20961770.193833323509
2.0155-2.05430.22281360.199733983534
2.0543-2.09620.21781430.201933833526
2.0962-2.14180.25491820.202933333515
2.1418-2.19160.24381760.198233803556
2.1916-2.24650.23411550.198133603515
2.2465-2.30720.25421620.195133813543
2.3072-2.37510.19591870.204533643551
2.3751-2.45170.24641960.194533423538
2.4517-2.53940.24982130.194333283541
2.5394-2.6410.24221600.196834073567
2.641-2.76120.23241770.191633643541
2.7612-2.90670.23181380.191834273565
2.9067-3.08880.21492000.180833663566
3.0888-3.32720.1851990.167633973596
3.3272-3.66190.19191760.157134133589
3.6619-4.19150.16771630.143234553618
4.1915-5.27950.12882070.120734483655
5.2795-44.52730.17682270.163735773804

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