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- PDB-7amf: Crystal structure of rsFolder2 in its non-fluorescent off-state -

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Basic information

Entry
Database: PDB / ID: 7amf
TitleCrystal structure of rsFolder2 in its non-fluorescent off-state
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / GFP / Reversibly Photoswitchable Fluorescent Protein / Photoconvertible FP
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 / Resolution: 1.63 Å
AuthorsMoreno-Chicano, T. / El Khatib, M. / Colletier, J.-P.
CitationJournal: Chemphyschem / Year: 2022
Title: Rational Control of Off-State Heterogeneity in a Photoswitchable Fluorescent Protein Provides Switching Contrast Enhancement.
Authors: Adam, V. / Hadjidemetriou, K. / Jensen, N. / Shoeman, R.L. / Woodhouse, J. / Aquila, A. / Banneville, A.S. / Barends, T.R.M. / Bezchastnov, V. / Boutet, S. / Byrdin, M. / Cammarata, M. / ...Authors: Adam, V. / Hadjidemetriou, K. / Jensen, N. / Shoeman, R.L. / Woodhouse, J. / Aquila, A. / Banneville, A.S. / Barends, T.R.M. / Bezchastnov, V. / Boutet, S. / Byrdin, M. / Cammarata, M. / Carbajo, S. / Eleni Christou, N. / Coquelle, N. / De la Mora, E. / El Khatib, M. / Moreno Chicano, T. / Bruce Doak, R. / Fieschi, F. / Foucar, L. / Glushonkov, O. / Gorel, A. / Grunbein, M.L. / Hilpert, M. / Hunter, M. / Kloos, M. / Koglin, J.E. / Lane, T.J. / Liang, M. / Mantovanelli, A. / Nass, K. / Nass Kovacs, G. / Owada, S. / Roome, C.M. / Schiro, G. / Seaberg, M. / Stricker, M. / Thepaut, M. / Tono, K. / Ueda, K. / Uriarte, L.M. / You, D. / Zala, N. / Domratcheva, T. / Jakobs, S. / Sliwa, M. / Schlichting, I. / Colletier, J.P. / Bourgeois, D. / Weik, M.
History
DepositionOct 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 2.0Oct 19, 2022Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy
Category: atom_site / citation ...atom_site / citation / citation_author / entity_src_gen / pdbx_nonpoly_scheme / pdbx_struct_mod_residue / 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 / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _entity_src_gen.gene_src_common_name / _pdbx_nonpoly_scheme.auth_seq_num / _struct_ref_seq_dif.details / _struct_ref_seq_dif.mon_id / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_ref_seq_dif.seq_num
Revision 2.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)107,1737
Polymers106,8964
Non-polymers2763
Water17,673981
1
A: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)26,7241
Polymers26,7241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8162
Polymers26,7241
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8162
Polymers26,7241
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8162
Polymers26,7241
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)142.300, 134.910, 51.660
Angle α, β, γ (deg.)90.000, 105.970, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-31-

ARG

21A-311-

HOH

31A-474-

HOH

41B-434-

HOH

51C-576-

HOH

61D-470-

HOH

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Components

#1: Protein
Green fluorescent protein /


Mass: 26724.070 Da / Num. of mol.: 4
Mutation: S30R, Y39N, F64L, S65A, Q69L, Q80R, F99S, N105T, M153T, V163S, I171V, A206K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P42212
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 981 / 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: 2.22 Å3/Da / Density % sol: 44.5 % / Description: Large thick plate
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 20% PEG 3350, 100 mM Tris pH 8.5, 20 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.63→48.12 Å / Num. obs: 116053 / % possible obs: 99.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 18.45 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.072 / Χ2: 0.97 / Net I/σ(I): 11.3
Reflection shellResolution: 1.63→1.66 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 5765 / CC1/2: 0.679 / Rrim(I) all: 0.807 / Χ2: 0.95 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
REFMAC5.8.0258phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5dtz

5dtz


Resolution: 1.63→48.12 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.276 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1927 2000 1.7 %RANDOM
Rwork0.1544 ---
obs0.1551 114053 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 101.14 Å2 / Biso mean: 24.197 Å2 / Biso min: 7.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å20 Å20.07 Å2
2--1.65 Å20 Å2
3----0.79 Å2
Refinement stepCycle: final / Resolution: 1.63→48.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7422 0 18 984 8424
Biso mean--69.01 39.1 -
Num. residues----931
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0138858
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177888
X-RAY DIFFRACTIONr_angle_refined_deg2.011.68712092
X-RAY DIFFRACTIONr_angle_other_deg1.4471.60918480
X-RAY DIFFRACTIONr_dihedral_angle_1_deg15.0765.2421156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.85823.377456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.445151499
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6671542
X-RAY DIFFRACTIONr_chiral_restr0.0810.21106
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211093
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021864
LS refinement shellResolution: 1.63→1.672 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 147 -
Rwork0.301 8384 -
all-8531 -
obs--99.46 %

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