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- PDB-3ssp: Engineered low-affinity halide-binding protein derived from YFP: ... -

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Basic information

Entry
Database: PDB / ID: 3ssp
TitleEngineered low-affinity halide-binding protein derived from YFP: halide-free
ComponentsGreen fluorescent protein
KeywordsHALIDE BINDING PROTEIN / beta barrel / luminescent protein / yellow fluorescent protein / imaging reagent
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: 1.628 Å
AuthorsWang, W. / Grimley, J.S. / Beese, L.S. / Hellinga, H.W.
CitationJournal: To be Published
Title: Determination of engineered chloride-binding site structures in fluorescent proteins reveals principles of halide recognition
Authors: Wang, W. / Grimley, J.S. / Augustine, G.J. / Beese, L.S. / Hellinga, H.W.
History
DepositionJul 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 2.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)29,3631
Polymers29,3631
Non-polymers00
Water5,855325
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.254, 62.603, 69.792
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: 29362.801 Da / Num. of mol.: 1 / Mutation: S72A, K79R, T203Y, H231L
Source method: isolated from a genetically manipulated source
Details: synthetic / Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): KRX / References: UniProt: P42212
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsUNP RESIDUE SER65 UNDERWENT MUTATION TO GLY. GLY65, TYR66, AND GLY67 CIRCULARIZED INTO ONE CHROMOPHORE (CR2).

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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: 1.91 Å3/Da / Density % sol: 35.49 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 14% PEG4000, 50 mM sodium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 17, 2009
RadiationMonochromator: Rosenbaum-Rock double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.628→41.311 Å / Num. obs: 27845 / % possible obs: 96.8 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.098 / Χ2: 1.535 / Net I/σ(I): 17.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.63-1.663.60.2313461.172196.6
1.66-1.694.10.21514021.279198.9
1.69-1.724.10.19614131.265199.2
1.72-1.764.20.18414061.26199.2
1.76-1.794.20.16414001.207199.2
1.79-1.844.30.15113971.218198.8
1.84-1.884.30.13914001.33198.2
1.88-1.934.30.12313901.186198.2
1.93-1.994.30.1113761.281198.1
1.99-2.054.40.114111.383197.9
2.05-2.134.30.09413971.135197.9
2.13-2.214.40.09313751.956197.2
2.21-2.314.40.08713971.189196.7
2.31-2.434.40.0813911.537196.6
2.43-2.594.40.07213650.841196.5
2.59-2.794.40.07514021.655196.5
2.79-3.074.60.08813813.198195.1
3.07-3.514.80.09513931.041194.9
3.51-4.424.90.09813812.235192.9
4.42-504.80.09714222.814189.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3SST

3sst


Resolution: 1.628→39.658 Å / Occupancy max: 1 / Occupancy min: 0.3 / SU ML: 0.32 / σ(F): 1.34 / Phase error: 15.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1742 1399 5.03 %
Rwork0.1458 --
obs0.1473 27786 96.48 %
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.722 Å2 / ksol: 0.424 e/Å3
Displacement parametersBiso max: 108.19 Å2 / Biso mean: 16.7294 Å2 / Biso min: 4.31 Å2
Baniso -1Baniso -2Baniso -3
1--1.7708 Å2-0 Å20 Å2
2---0.6978 Å2-0 Å2
3---2.4686 Å2
Refinement stepCycle: LAST / Resolution: 1.628→39.658 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1837 0 0 325 2162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091979
X-RAY DIFFRACTIONf_angle_d1.3922691
X-RAY DIFFRACTIONf_chiral_restr0.089286
X-RAY DIFFRACTIONf_plane_restr0.006360
X-RAY DIFFRACTIONf_dihedral_angle_d15.579739
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.628-1.68620.21161410.17452511265294
1.6862-1.75370.18861510.16152670282199
1.7537-1.83350.17731450.14932670281599
1.8335-1.93020.19221280.13632651277998
1.9302-2.05110.1591270.1332665279298
2.0511-2.20950.17211290.13522660278997
2.2095-2.43180.19361330.14482645277897
2.4318-2.78360.15731610.14622624278596
2.7836-3.50670.18571450.14132629277495
3.5067-39.66980.15591390.15192662280191

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