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- PDB-5du0: Crystal structure of rsFolder in the non-fluorescent off-state -

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Basic information

Entry
Database: PDB / ID: 5du0
TitleCrystal structure of rsFolder in the non-fluorescent off-state
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / GFP / reversibly switchable / trans 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
Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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 1.1Sep 20, 2017Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.2Jan 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


Theoretical massNumber of molelcules
Total (without water)118,7144
Polymers118,7144
Non-polymers00
Water3,711206
1
A: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)29,6781
Polymers29,6781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)29,6781
Polymers29,6781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)29,6781
Polymers29,6781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)29,6781
Polymers29,6781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)141.290, 134.800, 51.050
Angle α, β, γ (deg.)90.00, 105.58, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-31-

ARG

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Components

#1: Protein
Green fluorescent protein


Mass: 29678.436 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / References: UniProt: P42212
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.27 Å3/Da / Density % sol: 45.83 %
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: 0.992 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.992 Å / Relative weight: 1
ReflectionResolution: 2.35→95.77 Å / Num. obs: 37525 / % possible obs: 98.07 % / Redundancy: 4 % / Rsym value: 0.104 / Net I/σ(I): 10.1
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.2 / % possible all: 88.56

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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: 2.35→95.77 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.917 / SU B: 10.091 / SU ML: 0.231 / Cross valid method: THROUGHOUT / ESU R: 0.574 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25734 1877 5 %RANDOM
Rwork0.20832 ---
obs0.21075 35647 98.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.456 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0 Å20 Å2
2--0.02 Å2-0 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.35→95.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7261 0 0 206 7467
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0197440
X-RAY DIFFRACTIONr_bond_other_d0.0020.027040
X-RAY DIFFRACTIONr_angle_refined_deg1.0541.96710048
X-RAY DIFFRACTIONr_angle_other_deg1.8253.00216260
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4245900
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.78224.831356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.694151296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5091532
X-RAY DIFFRACTIONr_chiral_restr0.0610.21092
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218388
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021696
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_it3.4283.8583624
X-RAY DIFFRACTIONr_mcbond_other3.4293.8573623
X-RAY DIFFRACTIONr_mcangle_it4.9645.7794516
X-RAY DIFFRACTIONr_mcangle_other4.9645.7814517
X-RAY DIFFRACTIONr_scbond_it4.2914.3063815
X-RAY DIFFRACTIONr_scbond_other4.294.3083816
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7226.2525531
X-RAY DIFFRACTIONr_long_range_B_refined9.06930.5498054
X-RAY DIFFRACTIONr_long_range_B_other9.07130.5288002
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.351→2.412 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.488 120 -
Rwork0.334 2272 -
obs--84.64 %

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