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- PDB-4xov: Structure of rsGreen0.7 in the green-off-state -

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Basic information

Entry
Database: PDB / ID: 4xov
TitleStructure of rsGreen0.7 in the green-off-state
ComponentsrsGreen0.7
KeywordsFLUORESCENT PROTEIN / Green Fluorescent Proteins / Reversible photoswitchablility
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: 1.2 Å
AuthorsDe Zitter, E. / Van Meervelt, L.
Funding support Belgium, 1items
OrganizationGrant numberCountry
IWT Belgium
CitationJournal: Acs Nano / Year: 2015
Title: Expression-Enhanced Fluorescent Proteins Based on Enhanced Green Fluorescent Protein for Super-resolution Microscopy.
Authors: Duwe, S. / De Zitter, E. / Gielen, V. / Moeyaert, B. / Vandenberg, W. / Grotjohann, T. / Clays, K. / Jakobs, S. / Van Meervelt, L. / Dedecker, P.
History
DepositionJan 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Sep 23, 2015Group: Database references
Revision 1.3Nov 4, 2015Group: Database references
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: rsGreen0.7


Theoretical massNumber of molelcules
Total (without water)30,6691
Polymers30,6691
Non-polymers00
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.992, 61.308, 105.739
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 rsGreen0.7 / Green fluorescent protein


Mass: 30669.439 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) / Strain (production host): JM109 / References: UniProt: P42212
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O

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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 % sol: 27.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 0.15 M NaBr, 30% PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.2→40.04 Å / Num. obs: 125686 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 13.81 Å2 / Rmerge(I) obs: 0.157 / Net I/σ(I): 4.9
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.613 / Mean I/σ(I) obs: 1.4 / Num. unique all: 12598 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
XSCALEdata scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→40.038 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 15.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1683 3813 3.03 %Random Selection
Rwork0.1431 121864 --
obs0.1439 125677 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 141.56 Å2 / Biso mean: 21.8065 Å2 / Biso min: 4.36 Å2
Refinement stepCycle: final / Resolution: 1.2→40.038 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1813 0 0 291 2104
Biso mean---32.32 -
Num. residues----228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092178
X-RAY DIFFRACTIONf_angle_d1.3492988
X-RAY DIFFRACTIONf_chiral_restr0.077316
X-RAY DIFFRACTIONf_plane_restr0.007406
X-RAY DIFFRACTIONf_dihedral_angle_d13.863820
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.2-1.21520.26341420.237145594701
1.2152-1.23120.27891450.231145614706
1.2312-1.24810.23241370.224644064543
1.2481-1.26590.25141390.207745574696
1.2659-1.28480.23721440.201845054649
1.2848-1.30490.20141410.196245264667
1.3049-1.32630.21851440.180145464690
1.3263-1.34910.20141400.186144544594
1.3491-1.37370.18731420.167845174659
1.3737-1.40010.18321440.158145024646
1.4001-1.42870.19631430.153545044647
1.4287-1.45970.16231370.147445494686
1.4597-1.49370.17951420.13644944636
1.4937-1.53110.14771410.129645414682
1.5311-1.57250.19591400.131245014641
1.5725-1.61870.15791420.126144854627
1.6187-1.6710.15011410.127645324673
1.671-1.73070.16411420.12545214663
1.7307-1.80.14561420.129544694611
1.8-1.88190.16131420.125345794721
1.8819-1.98110.16651390.120544824621
1.9811-2.10520.14171390.118745254664
2.1052-2.26780.16221440.126445174661
2.2678-2.4960.1571380.138344904628
2.496-2.8570.18941440.149645274671
2.857-3.59920.17111390.140745114650
3.5992-40.06040.14251400.148345044644

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