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- PDB-7a8g: rsGreen0.7-K206A-H148G in the green-on state -

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Basic information

Entry
Database: PDB / ID: 7a8g
TitlersGreen0.7-K206A-H148G 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 / TRIETHYLENE GLYCOL / Green fluorescent protein
Function and homology information
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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 ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2113
Polymers61,0602
Non-polymers1501
Water4,594255
1
A: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)30,5301
Polymers30,5301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6802
Polymers30,5301
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.438, 88.622, 131.360
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 4 through 24 or resid 27...
21(chain B and (resid 4 through 24 or resid 27...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYGLYGLY(chain A and (resid 4 through 24 or resid 27...AA4 - 2438 - 58
12PHEPHEVALVAL(chain A and (resid 4 through 24 or resid 27...AA27 - 2961 - 63
13GLYGLYLYSLYS(chain A and (resid 4 through 24 or resid 27...AA31 - 7965 - 111
14HISHISPROPRO(chain A and (resid 4 through 24 or resid 27...AA81 - 89113 - 121
15GLYGLYILEILE(chain A and (resid 4 through 24 or resid 27...AA4 - 22938 - 261
16GLYGLYLYSLYS(chain A and (resid 4 through 24 or resid 27...AA127 - 131159 - 163
17ILEILEASPASP(chain A and (resid 4 through 24 or resid 27...AA152 - 155184 - 187
18GLYGLYILEILE(chain A and (resid 4 through 24 or resid 27...AA4 - 22938 - 261
19GLYGLYILEILE(chain A and (resid 4 through 24 or resid 27...AA4 - 22938 - 261
110GLYGLYILEILE(chain A and (resid 4 through 24 or resid 27...AA4 - 22938 - 261
111GLYGLYILEILE(chain A and (resid 4 through 24 or resid 27...AA4 - 22938 - 261
21GLYGLYGLYGLY(chain B and (resid 4 through 24 or resid 27...BB4 - 2438 - 58
22PHEPHEVALVAL(chain B and (resid 4 through 24 or resid 27...BB27 - 2961 - 63
23GLYGLYLYSLYS(chain B and (resid 4 through 24 or resid 27...BB31 - 7965 - 111
24GLYGLYILEILE(chain B and (resid 4 through 24 or resid 27...BB4 - 22938 - 261
25GLYGLYALAALA(chain B and (resid 4 through 24 or resid 27...BB134 - 150166 - 182
26GLYGLYILEILE(chain B and (resid 4 through 24 or resid 27...BB4 - 22938 - 261
27ILEILELYSLYS(chain B and (resid 4 through 24 or resid 27...BB152 - 158184 - 190
28ASNASNASPASP(chain B and (resid 4 through 24 or resid 27...BB205 - 21237 - 55
29ASPASPILEILE(chain B and (resid 4 through 24 or resid 27...BB216 - 229248 - 261

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Components

#1: Protein Green fluorescent protein


Mass: 30530.244 Da / Num. of mol.: 2
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-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.85 Å3/Da / Density % sol: 56.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 200 mM TMAO 100mM Tris pH 8.5 20 % Peg 2000 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: 2→49.44 Å / Num. obs: 39875 / % possible obs: 99.9 % / Redundancy: 7.5 % / Biso Wilson estimate: 29.62 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.022 / Rrim(I) all: 0.06 / Net I/σ(I): 19.9 / Num. measured all: 297790 / Scaling rejects: 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
2-2.057.70.6162242529080.9650.2390.6623.599.9
8.94-49.445.60.02629785300.9990.0110.02858.698.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.37 Å49.44 Å
Translation4.37 Å49.44 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.6.1data scaling
PHASER2.7.16phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→49.438 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2171 2061 5.19 %
Rwork0.1794 37655 -
obs0.1814 39716 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.09 Å2 / Biso mean: 35.4456 Å2 / Biso min: 19.15 Å2
Refinement stepCycle: final / Resolution: 2→49.438 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3548 0 10 255 3813
Biso mean--60.26 41.11 -
Num. residues----448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073774
X-RAY DIFFRACTIONf_angle_d0.9155121
X-RAY DIFFRACTIONf_chiral_restr0.061544
X-RAY DIFFRACTIONf_plane_restr0.005680
X-RAY DIFFRACTIONf_dihedral_angle_d10.9593033
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1928X-RAY DIFFRACTION6.103TORSIONAL
12B1928X-RAY DIFFRACTION6.103TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.04650.32931320.27522474260699
2.0465-2.09770.30741100.2532471258199
2.0977-2.15440.31421100.23192517262799
2.1544-2.21780.32161290.218724732602100
2.2178-2.28940.26531400.217524522592100
2.2894-2.37120.24031250.197825212646100
2.3712-2.46620.2511340.192124832617100
2.4662-2.57840.27021460.187224632609100
2.5784-2.71430.23681470.196524972644100
2.7143-2.88440.23571490.202824982647100
2.8844-3.10710.21291620.200124842646100
3.1071-3.41970.24961370.180925252662100
3.4197-3.91430.2041520.170525362688100
3.9143-4.93090.16651420.133125802722100
4.9309-49.45310.16341460.15572681282799

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