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- PDB-5dtz: Crystal structure of rsFolder in the fluorescent on-state -

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Basic information

Entry
Database: PDB / ID: 5dtz
TitleCrystal structure of rsFolder in the fluorescent on-state
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / GFP / reversibly switchable / cis chromophore
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
DI(HYDROXYETHYL)ETHER / Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsEl Khatib, M. / Colletier, J.P. / Adam, V.
CitationJournal: Sci Rep / Year: 2016
Title: Rational design of ultrastable and reversibly photoswitchable fluorescent proteins for super-resolution imaging of the bacterial periplasm.
Authors: El Khatib, M. / Martins, A. / Bourgeois, D. / Colletier, J.P. / Adam, V.
History
DepositionSep 18, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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)117,8157
Polymers117,4964
Non-polymers3183
Water18,0871004
1
A: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)29,3741
Polymers29,3741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)29,3741
Polymers29,3741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4802
Polymers29,3741
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5863
Polymers29,3741
Non-polymers2122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)142.470, 134.560, 51.720
Angle α, β, γ (deg.)90.00, 106.05, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-603-

HOH

21D-417-

HOH

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Components

#1: Protein
Green fluorescent protein


Mass: 29374.113 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: plasmid / Details (production host): pET15-b / Production host: Escherichia coli (E. coli) / References: UniProt: P42212
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1004 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.5→95.97 Å / Num. obs: 144849 / % possible obs: 97.12 % / Redundancy: 4 % / Rsym value: 0.078 / Net I/σ(I): 9
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.1 / % possible all: 81.62

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B3P

2b3p


Resolution: 1.5→95.97 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.804 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2016 7243 5 %RANDOM
Rwork0.17379 ---
obs0.17518 137606 97.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.652 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→95.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7351 0 21 1004 8376
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0197626
X-RAY DIFFRACTIONr_bond_other_d0.0010.027227
X-RAY DIFFRACTIONr_angle_refined_deg1.3961.96810309
X-RAY DIFFRACTIONr_angle_other_deg0.6273.00216702
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7135934
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.47724.699366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.487151331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5951535
X-RAY DIFFRACTIONr_chiral_restr0.0930.21118
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0218601
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021746
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8342.0943688
X-RAY DIFFRACTIONr_mcbond_other2.8262.0933687
X-RAY DIFFRACTIONr_mcangle_it3.8273.134602
X-RAY DIFFRACTIONr_mcangle_other3.8273.1324603
X-RAY DIFFRACTIONr_scbond_it4.2962.5233938
X-RAY DIFFRACTIONr_scbond_other4.2962.5233939
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4963.5795696
X-RAY DIFFRACTIONr_long_range_B_refined8.71518.9019105
X-RAY DIFFRACTIONr_long_range_B_other8.63217.8938539
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.491 438 -
Rwork0.478 8310 -
obs--79.53 %

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