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- PDB-5hw9: Filamentous Assembly of Green Fluorescent Protein Supported by a ... -

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Basic information

Entry
Database: PDB / ID: 5hw9
TitleFilamentous Assembly of Green Fluorescent Protein Supported by a C-terminal fusion of 18-residues, viewed in space group P21
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 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 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Nov 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

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Assembly

Deposited unit
A: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)28,9511
Polymers28,9511
Non-polymers00
Water1086
1
A: Green fluorescent protein

A: Green fluorescent protein

A: Green fluorescent protein

A: Green fluorescent protein

A: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)144,7535
Polymers144,7535
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation2_655-x+1,y+1/2,-z1
crystal symmetry operation2_645-x+1,y-1/2,-z1
Unit cell
Length a, b, c (Å)45.730, 51.800, 54.790
Angle α, β, γ (deg.)90.000, 95.960, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is a filament with 2 sub 1 screw symmetry. The contents of REMARK 350 represent a portion of that filament

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Components

#1: Protein Green fluorescent protein


Mass: 28950.619 Da / Num. of mol.: 1 / Mutation: S65A, V68L, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.23 Å3/Da / Density % sol: 44.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% 1,6-hexanediol, sodium cacodylate pH 6.5, 5 mM magnesium chloride, 200 mM KCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.476 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.476 Å / Relative weight: 1
ReflectionResolution: 3→45.48 Å / Num. all: 4965 / Num. obs: 4965 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.189 / Net I/σ(I): 5.81
Reflection shellResolution: 3→3.08 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 1.24 / % possible all: 84.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASER2.5.6phasing
BUSTER-TNTrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HBD

5hbd


Resolution: 3→45.48 Å / Cor.coef. Fo:Fc: 0.9251 / Cor.coef. Fo:Fc free: 0.8763 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.43
RfactorNum. reflection% reflectionSelection details
Rfree0.2322 502 10.11 %RANDOM
Rwork0.1864 ---
obs0.1911 4963 95.11 %-
Displacement parametersBiso max: 125.35 Å2 / Biso mean: 49.98 Å2 / Biso min: 24.62 Å2
Baniso -1Baniso -2Baniso -3
1--2.0812 Å20 Å2-3.3864 Å2
2---0.3722 Å20 Å2
3---2.4534 Å2
Refine analyzeLuzzati coordinate error obs: 0.425 Å
Refinement stepCycle: final / Resolution: 3→45.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1952 0 0 6 1958
Biso mean---37.88 -
Num. residues----245
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d713SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes56HARMONIC2
X-RAY DIFFRACTIONt_gen_planes284HARMONIC5
X-RAY DIFFRACTIONt_it1998HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion252SEMIHARMONIC5
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_contact2145SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1998HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2694HARMONIC21.22
X-RAY DIFFRACTIONt_omega_torsion3.99
X-RAY DIFFRACTIONt_other_torsion17.87
LS refinement shellResolution: 3→3.35 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2838 134 10.13 %
Rwork0.2286 1189 -
all0.2342 1323 -
obs--95.11 %
Refinement TLS params.Method: refined / Origin x: 12.4192 Å / Origin y: -1.3441 Å / Origin z: 6.7312 Å
111213212223313233
T-0.042 Å2-0.0014 Å2-0.1032 Å2--0.0506 Å20.0062 Å2---0.014 Å2
L0.3481 °20.1756 °20.2237 °2-1.0099 °20.5307 °2--0.6204 °2
S-0.0224 Å °0.0116 Å °0.0353 Å °0.0151 Å °-0.0605 Å °-0.0031 Å °-0.1205 Å °-0.0397 Å °0.0829 Å °
Refinement TLS groupSelection details: { A|* }

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