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

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Basic information

Entry
Database: PDB / ID: 3sve
TitleEngineered low-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: 1.492 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 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 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 2.1Oct 9, 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)29,6034
Polymers29,3631
Non-polymers2403
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.296, 62.212, 69.549
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-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.: 252 / 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: 34.91 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 18% 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: 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: 1.492→41.282 Å / Num. obs: 36416 / % possible obs: 98.8 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.077 / Χ2: 1.053 / Net I/σ(I): 13.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.5-1.534.90.46816510.874190.3
1.53-1.555.50.46217170.969195.2
1.55-1.5860.42517790.879198
1.58-1.626.60.36317970.914198.3
1.62-1.657.10.34917860.947199.7
1.65-1.697.30.29217990.956199.1
1.69-1.737.40.24818041.008199
1.73-1.787.40.22618001.045199.2
1.78-1.837.40.1818291.144199.9
1.83-1.897.40.14418081.196199.5
1.89-1.967.40.11918181.067199.6
1.96-2.047.40.10118221.225199.7
2.04-2.137.40.08718321.262199.7
2.13-2.247.30.0818531.153199.7
2.24-2.387.30.07618231.078199.9
2.38-2.567.20.07118461.114199.8
2.56-2.827.10.06918671.074199.9
2.82-3.2370.06218800.971199.9
3.23-4.076.90.05718880.9671100
4.07-506.30.06120171.026199.8

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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: 1.492→34.775 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.28 / σ(F): 1.34 / Phase error: 16.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1787 1836 5.05 %
Rwork0.153 --
obs0.1543 36359 98.51 %
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.23 Å2 / ksol: 0.406 e/Å3
Displacement parametersBiso max: 125.32 Å2 / Biso mean: 22.5524 Å2 / Biso min: 8.68 Å2
Baniso -1Baniso -2Baniso -3
1--2.9232 Å2-0 Å20 Å2
2---0.3935 Å2-0 Å2
3---3.3168 Å2
Refinement stepCycle: LAST / Resolution: 1.492→34.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1837 0 3 252 2092
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0191948
X-RAY DIFFRACTIONf_angle_d1.822645
X-RAY DIFFRACTIONf_chiral_restr0.107281
X-RAY DIFFRACTIONf_plane_restr0.011351
X-RAY DIFFRACTIONf_dihedral_angle_d15.015724
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4922-1.53250.27511240.21942348247288
1.5325-1.57760.25241240.20262595271997
1.5776-1.62860.23281580.17412586274499
1.6286-1.68680.18991450.1552642278799
1.6868-1.75430.18491430.15162628277199
1.7543-1.83410.18081450.15172678282399
1.8341-1.93080.18761260.141426552781100
1.9308-2.05180.17861350.138926852820100
2.0518-2.21020.15611330.142726942827100
2.2102-2.43260.17551420.147726922834100
2.4326-2.78440.16131570.151827022859100
2.7844-3.50750.1951550.147227352890100
3.5075-34.78390.1591490.156728833032100

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