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

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Basic information

Entry
Database: PDB / ID: 3sst
TitleEngineered low-affinity halide-binding protein derived from YFP: chloride 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
Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.403 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: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.2Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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 27, 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)29,3982
Polymers29,3631
Non-polymers351
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.494, 62.688, 69.764
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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 1.92 Å3/Da / Density % sol: 35.85 %
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: 1.403→41.43 Å / Num. obs: 39190 / % possible obs: 87.4 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.075 / Χ2: 1.518 / Net I/σ(I): 13.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.4-1.423.40.4919120.957186.5
1.42-1.453.70.49619591.075189
1.45-1.483.90.4219791.127189.3
1.48-1.514.10.38719741.159189.6
1.51-1.544.30.34519841.269190
1.54-1.584.50.34419641.432189.3
1.58-1.624.60.28819941.572188.7
1.62-1.664.80.27719611.615188.8
1.66-1.714.90.25119811.848189.7
1.71-1.7650.2520162.413190.3
1.76-1.835.10.21120132.312190.2
1.83-1.95.10.17119932.045189.6
1.9-1.995.20.13519901.843189.2
1.99-2.095.20.11219811.467188.8
2.09-2.225.20.09819891.471188.2
2.22-2.395.20.08919401.326186.6
2.39-2.635.30.07419351.256185.7
2.63-3.025.30.06719211.245183.7
3.02-3.85.30.05718651.197181.1
3.8-505.10.05418391.055175.1

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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
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2O24

2o24


Resolution: 1.403→34.882 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.25 / σ(F): 1.33 / Phase error: 17.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1822 1976 5.06 %
Rwork0.1609 --
obs0.1621 39041 86.97 %
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.281 Å2 / ksol: 0.447 e/Å3
Displacement parametersBiso max: 120.44 Å2 / Biso mean: 24.4996 Å2 / Biso min: 11.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.9375 Å2-0 Å20 Å2
2---0.6254 Å2-0 Å2
3---1.5629 Å2
Refinement stepCycle: LAST / Resolution: 1.403→34.882 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1837 0 1 266 2104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121931
X-RAY DIFFRACTIONf_angle_d1.4882619
X-RAY DIFFRACTIONf_chiral_restr0.086279
X-RAY DIFFRACTIONf_plane_restr0.007346
X-RAY DIFFRACTIONf_dihedral_angle_d15.138716
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.403-1.43810.25691290.22832538266785
1.4381-1.4770.24271290.20862662279189
1.477-1.52050.22551540.19522692284689
1.5205-1.56950.21951340.18432689282389
1.5695-1.62560.22151580.17492645280389
1.6256-1.69070.21011460.17032668281489
1.6907-1.76770.19251460.16952712285890
1.7677-1.86080.17711500.16282687283790
1.8608-1.97740.17891270.15672734286189
1.9774-2.13010.20581370.15762685282289
2.1301-2.34440.17611310.15752693282487
2.3444-2.68350.18291580.15732609276786
2.6835-3.38050.17611510.15262551270283
3.3805-34.89280.15771260.15462500262677

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