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- PDB-3ssl: Engineered high-affinity halide-binding protein derived from YFP:... -

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Basic information

Entry
Database: PDB / ID: 3ssl
TitleEngineered high-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: 1.449 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 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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

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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)29,9406
Polymers29,3061
Non-polymers6355
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.297, 62.741, 69.783
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: 29305.750 Da / Num. of mol.: 1 / Mutation: S72A, K79R, Q183A, 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 / Iodide


Mass: 126.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O
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: 1.92 Å3/Da / Density % sol: 35.8 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 17% PEG2000, 150 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: APS / Beamline: 22-ID / Wavelength: 1.1 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: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.449→34.515 Å / Num. obs: 40595 / % possible obs: 99.8 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 16.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.45-1.486.40.497199.2
1.48-1.56.60.414199.2
1.5-1.536.70.339199.8
1.53-1.566.70.304199.6
1.56-1.66.80.241199.7
1.6-1.636.80.205199.9
1.63-1.676.90.1751100
1.67-1.726.90.146199.9
1.72-1.7770.1291100
1.77-1.8370.1091100
1.83-1.897.10.0871100
1.89-1.977.10.0741100
1.97-2.067.20.0651100
2.06-2.177.20.0621100
2.17-2.37.20.061100
2.3-2.487.20.0541100
2.48-2.737.20.0481100
2.73-3.127.20.0431100
3.12-3.947.10.0381100
3.94-506.60.04199.5

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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
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.449→34.515 Å / Occupancy max: 1 / Occupancy min: 0.23 / SU ML: 0.33 / σ(F): 1.34 / Phase error: 15.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1765 2082 5.14 %
Rwork0.1341 --
obs0.1363 40526 99.6 %
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.309 Å2 / ksol: 0.439 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.6491 Å20 Å20 Å2
2--1.8364 Å2-0 Å2
3---0.8127 Å2
Refinement stepCycle: LAST / Resolution: 1.449→34.515 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1858 0 5 261 2124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011971
X-RAY DIFFRACTIONf_angle_d1.3212676
X-RAY DIFFRACTIONf_dihedral_angle_d15.028734
X-RAY DIFFRACTIONf_chiral_restr0.073286
X-RAY DIFFRACTIONf_plane_restr0.007352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4493-1.4830.21141250.16752430X-RAY DIFFRACTION96
1.483-1.52010.22331190.14492537X-RAY DIFFRACTION99
1.5201-1.56120.19381420.13312529X-RAY DIFFRACTION100
1.5612-1.60710.19171510.1172517X-RAY DIFFRACTION100
1.6071-1.6590.17741340.12062550X-RAY DIFFRACTION100
1.659-1.71830.18431250.10592545X-RAY DIFFRACTION100
1.7183-1.78710.18121590.11642516X-RAY DIFFRACTION100
1.7871-1.86840.14161520.10842531X-RAY DIFFRACTION100
1.8684-1.96690.1521490.1082566X-RAY DIFFRACTION100
1.9669-2.09010.15281230.10952575X-RAY DIFFRACTION100
2.0901-2.25140.1481310.11422584X-RAY DIFFRACTION100
2.2514-2.4780.17481330.12652598X-RAY DIFFRACTION100
2.478-2.83640.16851240.13392610X-RAY DIFFRACTION100
2.8364-3.5730.17421640.14372609X-RAY DIFFRACTION100
3.573-34.5250.2031510.16562747X-RAY DIFFRACTION100

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