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- PDB-8bgl: Structure of the dimeric rsCherryRev1.4 -

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Basic information

Entry
Database: PDB / ID: 8bgl
TitleStructure of the dimeric rsCherryRev1.4
ComponentsPAmCherry1 protein
KeywordsFLUORESCENT PROTEIN / dimerization / reversibly switchable / red fluorescent proteins / disulfide bond
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / DI(HYDROXYETHYL)ETHER / PAmCherry1 protein
Function and homology information
Biological speciesDiscosoma sp. (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBui, T.Y.H. / Van Meervelt, L.
Funding support Belgium, 2items
OrganizationGrant numberCountry
Other government911 project
KU Leuven Belgium
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2023
Title: An unusual disulfide-linked dimerization in the fluorescent protein rsCherryRev1.4.
Authors: Bui, T.Y.H. / Dedecker, P. / Van Meervelt, L.
History
DepositionOct 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.mon_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.ptnr1_label_atom_id
Revision 2.1Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 3.0Jul 24, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_mod_residue / pdbx_struct_special_symmetry / pdbx_validate_main_chain_plane / struct_asym / struct_conn / struct_ncs_dom_lim / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PAmCherry1 protein
B: PAmCherry1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5956
Polymers60,9512
Non-polymers6454
Water4,702261
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.104, 48.822, 99.120
Angle α, β, γ (deg.)90.000, 101.160, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11B-425-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5 through 31 or resid 33...
21(chain B and (resid 5 through 31 or resid 33...

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
11METMETGLYGLY(chain A and (resid 5 through 31 or resid 33...AA5 - 3143 - 69
12GLYGLYLEULEU(chain A and (resid 5 through 31 or resid 33...AA33 - 4671 - 84
13VALVALPHEPHE(chain A and (resid 5 through 31 or resid 33...AA48 - 6586 - 103
14LYSLYSPROPRO(chain A and (resid 5 through 31 or resid 33...AA70 - 88106 - 124
15GLYGLYPHEPHE(chain A and (resid 5 through 31 or resid 33...AA90 - 91126 - 127
16TRPTRPGLUGLU(chain A and (resid 5 through 31 or resid 33...AA93 - 148129 - 184
17METMETTYRTYR(chain A and (resid 5 through 31 or resid 33...AA150 - 214186 - 250
18ARGARGGLYGLY(chain A and (resid 5 through 31 or resid 33...AA216 - 219252 - 255
19ARGARGHISHIS(chain A and (resid 5 through 31 or resid 33...AA220 - 221256 - 257
21METMETGLYGLY(chain B and (resid 5 through 31 or resid 33...BB5 - 3143 - 69
22GLYGLYLEULEU(chain B and (resid 5 through 31 or resid 33...BB33 - 4671 - 84
23VALVALPHEPHE(chain B and (resid 5 through 31 or resid 33...BB48 - 6586 - 103
24LYSLYSPHEPHE(chain B and (resid 5 through 31 or resid 33...BB70 - 91106 - 127
25TRPTRPGLUGLU(chain B and (resid 5 through 31 or resid 33...BB93 - 148129 - 184
26METMETTYRTYR(chain B and (resid 5 through 31 or resid 33...BB150 - 181186 - 217
27ALAALATYRTYR(chain B and (resid 5 through 31 or resid 33...BB183 - 214219 - 250
28ARGARGHISHIS(chain B and (resid 5 through 31 or resid 33...BB216 - 221252 - 257

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Components

#1: Protein PAmCherry1 protein


Mass: 30475.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Chromophore structures : QYX, Q2K / Source: (gene. exp.) Discosoma sp. (sea anemone) / Gene: PAmCherry, PAmCherry1 / Production host: Escherichia coli (E. coli) / References: UniProt: D1MPT3
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O
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

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.71 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M MES pH 6.5, 12% w/v PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→76.17 Å / Num. obs: 31401 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 29.74 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.036 / Rrim(I) all: 0.093 / Net I/σ(I): 12.6 / Num. measured all: 212739
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
2-2.056.60.6131509123000.8940.2580.6672.899.9
8.94-76.1760.03623123870.9990.0160.0436.999.1

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H5Q

2h5q


Resolution: 2→62.62 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2314 1540 4.91 %
Rwork0.1882 29846 -
obs0.1903 31386 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.45 Å2 / Biso mean: 36.1371 Å2 / Biso min: 18.82 Å2
Refinement stepCycle: final / Resolution: 2→62.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3470 0 55 261 3786
Biso mean--42.06 41.32 -
Num. residues----434
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1946X-RAY DIFFRACTION3.789TORSIONAL
12B1946X-RAY DIFFRACTION3.789TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2-2.060.32371260.248426782804
2.06-2.140.27591280.233126992827
2.14-2.220.30081500.212426982848
2.22-2.330.24321450.201827092854
2.33-2.450.2811500.197526692819
2.45-2.60.27661150.205127242839
2.6-2.80.28681220.198327302852
2.8-3.080.24951720.203226842856
3.08-3.530.19971310.178427412872
3.53-4.450.19311740.161726992873
4.45-62.620.20941270.178428152942

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