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

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Basic information

Entry
Database: PDB / ID: 3ssk
TitleEngineered high-affinity halide-binding protein derived from YFP: bromide 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
BROMIDE ION / Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.361 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

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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)29,5454
Polymers29,3061
Non-polymers2403
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.379, 62.361, 69.629
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-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 1.9 Å3/Da / Density % sol: 35.16 %
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: 0.91993 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: 0.91993 Å / Relative weight: 1
ReflectionResolution: 1.361→46.454 Å / Num. all: 48667 / Num. obs: 47146

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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 3SRY

3sry


Resolution: 1.361→46.454 Å / Occupancy max: 1 / Occupancy min: 0.31 / SU ML: 0.25 / σ(F): 1.34 / Phase error: 16.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1715 2420 5.13 %
Rwork0.1294 --
obs0.1316 47136 96.97 %
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.065 Å2 / ksol: 0.447 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.0227 Å20 Å20 Å2
2--1.8833 Å2-0 Å2
3---1.1394 Å2
Refinement stepCycle: LAST / Resolution: 1.361→46.454 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1858 0 3 270 2131
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011936
X-RAY DIFFRACTIONf_angle_d1.2882623
X-RAY DIFFRACTIONf_dihedral_angle_d14.531720
X-RAY DIFFRACTIONf_chiral_restr0.074282
X-RAY DIFFRACTIONf_plane_restr0.007341
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.361-1.38930.3241250.21252320X-RAY DIFFRACTION87
1.3893-1.41950.24231290.16892548X-RAY DIFFRACTION95
1.4195-1.45250.23341420.15242534X-RAY DIFFRACTION96
1.4525-1.48880.20561210.1372608X-RAY DIFFRACTION97
1.4888-1.52910.20211290.12072609X-RAY DIFFRACTION97
1.5291-1.57410.18941570.11262605X-RAY DIFFRACTION97
1.5741-1.62490.19671390.10832615X-RAY DIFFRACTION98
1.6249-1.6830.16771480.10732621X-RAY DIFFRACTION98
1.683-1.75040.16361410.10732652X-RAY DIFFRACTION98
1.7504-1.830.17441630.10422620X-RAY DIFFRACTION98
1.83-1.92650.16311510.10362644X-RAY DIFFRACTION98
1.9265-2.04720.13911460.10392661X-RAY DIFFRACTION98
2.0472-2.20530.15481340.11082686X-RAY DIFFRACTION99
2.2053-2.42720.16891320.11982721X-RAY DIFFRACTION99
2.4272-2.77840.17871360.13512737X-RAY DIFFRACTION99
2.7784-3.50030.15051660.13272738X-RAY DIFFRACTION99
3.5003-46.48070.17811610.15262797X-RAY DIFFRACTION96

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