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- PDB-5hge: Filamentous Assembly of Green Fluorescent Protein Supported by a ... -

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Basic information

Entry
Database: PDB / ID: 5hge
TitleFilamentous Assembly of Green Fluorescent Protein Supported by a C-terminal fusion of 18-residues, viewed in space group P212121
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / filament / 2 sub 1 screw symmetry
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 / FOURIER SYNTHESIS / Resolution: 1.863 Å
Model detailsAn 18-residue C-terminal fusion forms an alpha helix which binds to surface of neighboring ...An 18-residue C-terminal fusion forms an alpha helix which binds to surface of neighboring protomer, supporting a filamentous assembly with 2 sub 1 screw symmetry
AuthorsSawaya, M.R. / Heller, D.M. / McPartland, L. / Hochschild, A. / Eisenberg, D.S.
CitationJournal: to be published
Title: Green Fluorescent Protein Fusion that Self Assembles as Polar Filaments
Authors: Sawaya, M.R. / Hochschild, A. / Heller, D.M. / McPartland, L. / Eisenberg, D.S.
History
DepositionJan 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software / Item: _software.classification
Revision 1.2Nov 1, 2017Group: Derived calculations / Category: pdbx_struct_assembly / Item: _pdbx_struct_assembly.method_details
Revision 1.3Sep 27, 2023Group: 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 / software / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0692
Polymers28,9511
Non-polymers1181
Water2,954164
1
A: Green fluorescent protein
hetero molecules

A: Green fluorescent protein
hetero molecules

A: Green fluorescent protein
hetero molecules

A: Green fluorescent protein
hetero molecules

A: Green fluorescent protein
hetero molecules

A: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,41312
Polymers173,7046
Non-polymers7096
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
crystal symmetry operation4_455x-1/2,-y+1/2,-z1
crystal symmetry operation4_655x+3/2,-y+1/2,-z1
Unit cell
Length a, b, c (Å)51.160, 62.910, 69.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Green fluorescent protein


Mass: 28950.619 Da / Num. of mol.: 1 / Mutation: S65A, V68L and S72A
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: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSER 65 WAS MUTATED TO ALA AND IS PART OF THE CHROMOPHORE PIA

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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: 1.92 Å3/Da / Density % sol: 36.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% MPD, 20% ethanol, 20 mM HEPES, pH 7.5, 10 mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.863→46.57 Å / Num. obs: 18522 / % possible obs: 96 % / Redundancy: 3.7 % / Biso Wilson estimate: 19.68 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.06 / Net I/σ(I): 9.4 / Num. measured all: 69078 / Scaling rejects: 1
Reflection shellResolution: 1.863→1.869 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 2 / Num. measured all: 10135 / Num. unique all: 2710 / CC1/2: 0.836 / Rpim(I) all: 0.317 / Rejects: 0 / % possible all: 96.6

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Processing

Software
NameVersionClassification
Aimless0.5.17data scaling
BUSTER-TNT2.10.0refinement
PDB_EXTRACT3.15data extraction
autoPROC1.0.4data scaling
BUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4PIQ

4piq


Resolution: 1.863→46.57 Å / Cor.coef. Fo:Fc: 0.9296 / Cor.coef. Fo:Fc free: 0.9059 / SU R Cruickshank DPI: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.156 / SU Rfree Blow DPI: 0.138 / SU Rfree Cruickshank DPI: 0.135
RfactorNum. reflection% reflectionSelection details
Rfree0.2114 1835 9.92 %RANDOM
Rwork0.1689 ---
obs0.1731 18492 95.38 %-
Displacement parametersBiso max: 161.68 Å2 / Biso mean: 24.94 Å2 / Biso min: 10.76 Å2
Baniso -1Baniso -2Baniso -3
1-8.5598 Å20 Å20 Å2
2--2.1383 Å20 Å2
3----10.698 Å2
Refine analyzeLuzzati coordinate error obs: 0.214 Å
Refinement stepCycle: final / Resolution: 1.863→46.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1937 0 8 165 2110
Biso mean--46.65 30.6 -
Num. residues----243
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d708SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes56HARMONIC2
X-RAY DIFFRACTIONt_gen_planes282HARMONIC5
X-RAY DIFFRACTIONt_it1990HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion251SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2336SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1990HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2685HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion4.01
X-RAY DIFFRACTIONt_other_torsion16.13
LS refinement shellResolution: 1.863→1.97 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2408 275 9.39 %
Rwork0.2056 2654 -
all0.2089 2929 -
obs--95.38 %
Refinement TLS params.Method: refined / Origin x: 1.3643 Å / Origin y: 3.8929 Å / Origin z: -4.0727 Å
111213212223313233
T-0.0411 Å2-0.0008 Å2-0.0073 Å2--0.0142 Å2-0.0032 Å2---0.006 Å2
L0.6634 °20.1853 °2-0.1367 °2-0.48 °2-0.0778 °2--0.0686 °2
S0.0124 Å °0.0191 Å °0.0376 Å °-0.0308 Å °-0.0098 Å °-0.0074 Å °0.0127 Å °0.0246 Å °-0.0026 Å °
Refinement TLS groupSelection details: { A|* }

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