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

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Basic information

Entry
Database: PDB / ID: 5hbd
TitleFilamentous Assembly of Green Fluorescent Protein Supported by a C-terminal fusion of 18-residues, viewed in space group C2
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / filament / 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: 1.65 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. / Hochschild, A. / Heller, D.M. / McPartland, L. / 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
DepositionDec 31, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software / Item: _software.classification
Revision 1.2Mar 6, 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)28,9511
Polymers28,9511
Non-polymers00
Water5,621312
1
A: Green fluorescent protein

A: Green fluorescent protein

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)202,6547
Polymers202,6547
Non-polymers00
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_575x,y+2,z1
crystal symmetry operation4_555-x+1/2,y+1/2,-z1
crystal symmetry operation4_545-x+1/2,y-1/2,-z1
crystal symmetry operation4_565-x+1/2,y+3/2,-z1
Unit cell
Length a, b, c (Å)112.700, 51.340, 55.060
Angle α, β, γ (deg.)90.00, 99.64, 90.00
Int Tables number5
Space group name H-MC121
SymmetryHelical symmetry: (Num. of operations: 100 / Rise per n subunits: 0.5 Å / Rotation per n subunits: 180 °)
Components on special symmetry positions
IDModelComponents
11A-505-

HOH

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Components

#1: Protein Green fluorescent protein


Mass: 28950.619 Da / Num. of mol.: 1 / Mutation: S65A, V68L
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.: 312 / 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: 2.71 Å3/Da / Density % sol: 54.55 % / Description: needle morphology
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M sodium citrate, 10% MPD, 0.1M HEPES, pH 7.5

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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: 1.65→55.62 Å / Num. obs: 34226 / % possible obs: 91.2 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 24.536 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.094 / Rrim(I) all: 0.103 / Χ2: 0.964 / Net I/σ(I): 13.65 / Num. measured all: 205218
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.65-1.752.90.7650.5342.2911206604038510.64563.8
1.75-1.870.8990.4484.0327367564052370.49592.9
1.87-2.020.9540.3596.6533807528951470.39197.3
2.02-2.210.9810.19710.8831349483947110.21497.4
2.21-2.470.9810.1713.0127751441342620.18596.6
2.47-2.850.9950.09219.2325875390138070.09997.6
2.85-3.490.9970.05926.9521335333532290.06496.8
3.49-4.920.9980.04733.4916615258625190.05197.4
4.920.9990.03635.319913148714630.0498.4

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Phasing

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

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XSCALEOct 15, 2015data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.15data extraction
autoPROC1.0.4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→55.62 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.773 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20475 3409 10 %RANDOM
Rwork0.17314 ---
obs0.17628 30817 91.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.999 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å20.6 Å2
2---0.7 Å2-0 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.65→55.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1921 0 0 312 2233
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191987
X-RAY DIFFRACTIONr_bond_other_d0.0030.021858
X-RAY DIFFRACTIONr_angle_refined_deg1.6961.9632683
X-RAY DIFFRACTIONr_angle_other_deg0.90734298
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6125243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.40125.35499
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.23415346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.781156
X-RAY DIFFRACTIONr_chiral_restr0.0890.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022257
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02457
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_it1.4071.564960
X-RAY DIFFRACTIONr_mcbond_other1.3941.562959
X-RAY DIFFRACTIONr_mcangle_it1.9392.3361198
X-RAY DIFFRACTIONr_mcangle_other1.9432.341199
X-RAY DIFFRACTIONr_scbond_it3.1271.9221027
X-RAY DIFFRACTIONr_scbond_other3.0941.9111025
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9722.7261482
X-RAY DIFFRACTIONr_long_range_B_refined7.32414.8752436
X-RAY DIFFRACTIONr_long_range_B_other6.96413.8092276
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 144 -
Rwork0.293 1409 -
obs--56.49 %
Refinement TLS params.Method: refined / Origin x: 17.2747 Å / Origin y: -0.6312 Å / Origin z: 6.5304 Å
111213212223313233
T0.0032 Å2-0.0018 Å20.0029 Å2-0.0122 Å2-0.0022 Å2--0.0043 Å2
L0.107 °2-0.0512 °20.0193 °2-0.1276 °20.0458 °2--0.0379 °2
S-0.007 Å °-0.0028 Å °0.0049 Å °0.0045 Å °0.0005 Å °0.0013 Å °0.0014 Å °-0.0087 Å °0.0065 Å °

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