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

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Basic information

Entry
Database: PDB / ID: 3ssy
TitleEngineered low-affinity halide-binding protein derived from YFP: iodide complex
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
IODIDE ION / Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.769 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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

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Assembly

Deposited unit
A: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7444
Polymers29,3631
Non-polymers3813
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.635, 61.821, 69.603
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 1.89 Å3/Da / Density % sol: 34.98 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 22% PEG2000, 50 mM sodium acetate, 90 mM magnesium chloride, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.1109 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2010
RadiationMonochromator: Rosenbaum-Rock double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1109 Å / Relative weight: 1
ReflectionResolution: 1.769→46.222 Å / Num. obs: 22178 / % possible obs: 99.1 % / Redundancy: 7 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 14
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.77-1.87.20.467198.2
1.8-1.837.20.427198.1
1.83-1.877.20.317198.4
1.87-1.917.20.3198.2
1.91-1.957.10.223199.3
1.95-1.997.20.197197.8
1.99-2.047.20.167199.6
2.04-2.17.20.139198.4
2.1-2.167.10.12198.7
2.16-2.237.10.105199.8
2.23-2.317.10.108199.2
2.31-2.47.10.082199.2
2.4-2.517.10.071199.4
2.51-2.6470.064199.5
2.64-2.816.90.059199.7
2.81-3.036.90.052199.8
3.03-3.336.80.038199.7
3.33-3.816.50.0281100
3.81-4.86.80.023198.8
4.8-506.70.027199.9

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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: 1.769→46.222 Å / Occupancy max: 1 / Occupancy min: 0.14 / SU ML: 0.32 / σ(F): 1.34 / Phase error: 18.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1939 1112 5.02 %
Rwork0.1561 --
obs0.158 22133 98.98 %
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.551 Å2 / ksol: 0.406 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.8617 Å20 Å2-0 Å2
2--4.9739 Å20 Å2
3----1.1122 Å2
Refinement stepCycle: LAST / Resolution: 1.769→46.222 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1833 0 3 234 2070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011937
X-RAY DIFFRACTIONf_angle_d1.2922629
X-RAY DIFFRACTIONf_dihedral_angle_d15.304719
X-RAY DIFFRACTIONf_chiral_restr0.088281
X-RAY DIFFRACTIONf_plane_restr0.006348
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7691-1.84970.20651330.17682499X-RAY DIFFRACTION97
1.8497-1.94720.23281310.16282592X-RAY DIFFRACTION99
1.9472-2.06920.20231240.14722611X-RAY DIFFRACTION98
2.0692-2.22890.18531400.14942599X-RAY DIFFRACTION99
2.2289-2.45320.20261380.14692609X-RAY DIFFRACTION99
2.4532-2.80820.181530.15392627X-RAY DIFFRACTION100
2.8082-3.53780.20021490.15112680X-RAY DIFFRACTION100
3.5378-46.23730.18431440.16342804X-RAY DIFFRACTION100

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