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- PDB-7a7z: rsGreen0.7-K206A-E222G in the green-on state -

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Basic information

Entry
Database: PDB / ID: 7a7z
TitlersGreen0.7-K206A-E222G 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: 1.1 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 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_close_contact
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_close_contact.auth_atom_id_2
Revision 2.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)30,5391
Polymers30,5391
Non-polymers00
Water9,116506
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.245, 61.556, 93.098
Angle α, β, γ (deg.)90.000, 97.410, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-663-

HOH

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Components

#1: Protein Green fluorescent protein


Mass: 30539.275 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 506 / 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: 2.7 Å3/Da / Density % sol: 54.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 200 mM (Li)2SO4 100 mM Tris pH 8.5 40 % PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 19, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.1→44.91 Å / Num. obs: 108890 / % possible obs: 99.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 12.85 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.029 / Rpim(I) all: 0.017 / Rrim(I) all: 0.033 / Net I/σ(I): 16.7
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
1.1-1.123.40.6231814853500.8790.3920.741.899.7
6.02-44.913.90.01727377000.9990.0090.01959.499.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.13 Å44.91 Å
Translation5.13 Å44.91 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: 1.1→40.402 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.45
RfactorNum. reflection% reflection
Rfree0.1424 5483 5.04 %
Rwork0.1225 --
obs0.1235 108725 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 72.86 Å2 / Biso mean: 20.0662 Å2 / Biso min: 4.43 Å2
Refinement stepCycle: final / Resolution: 1.1→40.402 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1784 0 0 506 2290
Biso mean---34.46 -
Num. residues----225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072307
X-RAY DIFFRACTIONf_angle_d1.0343182
X-RAY DIFFRACTIONf_chiral_restr0.084329
X-RAY DIFFRACTIONf_plane_restr0.007443
X-RAY DIFFRACTIONf_dihedral_angle_d23.811894
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1-1.11250.25081820.23023349353199
1.1125-1.12560.25821880.25383488367699
1.1256-1.13930.23271920.22183387357999
1.1393-1.15370.24831860.203334483634100
1.1537-1.16890.20931960.197734703666100
1.1689-1.18490.22341710.18233362353399
1.1849-1.20190.21021990.18413426362599
1.2019-1.21980.23381870.20043384357199
1.2198-1.23890.30751900.21343464365499
1.2389-1.25920.20681970.179733653562100
1.2592-1.28090.19821770.168234613638100
1.2809-1.30420.19331870.177434503637100
1.3042-1.32930.18411870.156834553642100
1.3293-1.35640.17881840.146534273611100
1.3564-1.38590.16821830.138334063589100
1.3859-1.41820.16211780.131634903668100
1.4182-1.45360.15911640.130134633627100
1.4536-1.49290.17151840.12553431361599
1.4929-1.53690.11711700.11473451362199
1.5369-1.58650.12661860.10723412359899
1.5865-1.64320.11891520.10534483600100
1.6432-1.7090.13712130.107434523665100
1.709-1.78670.15841830.109834503633100
1.7867-1.88090.12551680.109734923660100
1.8809-1.99880.10951730.11113423359699
1.9988-2.15310.12571930.10573439363299
2.1531-2.36980.13091540.1093450360499
2.3698-2.71260.14271910.10883464365599
2.7126-3.41730.12491760.105534953671100
3.4173-40.42910.11761920.115435403732100

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