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- PDB-3svb: Engineered medium-affinity halide-binding protein derived from YF... -

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Basic information

Entry
Database: PDB / ID: 3svb
TitleEngineered medium-affinity halide-binding protein derived from YFP: fluoride 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: 1.3 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: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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
Revision 2.1Oct 30, 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

Downloads & links

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Assembly

Deposited unit
A: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3702
Polymers29,3081
Non-polymers621
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.914, 63.194, 69.229
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: 29307.723 Da / Num. of mol.: 1 / Mutation: Q69T, S72A, K79R, V163A, 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 1.9 Å3/Da / Density % sol: 35.26 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 10% PEG3000, 150 mM ammonium acetate, pH 5.4, 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: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1109 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 54466 / % possible obs: 97.8 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.04 / Χ2: 0.933 / Net I/σ(I): 15.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.3-1.323.50.40920810.678176.2
1.32-1.354.10.38723770.674186.2
1.35-1.375.40.39926280.784196.2
1.37-1.46.50.34427390.722199.5
1.4-1.436.80.29827280.7421100
1.43-1.466.90.2627670.8161100
1.46-1.570.21527610.8151100
1.5-1.5470.17227500.879199.9
1.54-1.5970.13427560.8551100
1.59-1.647.10.11227560.8571100
1.64-1.77.10.08927660.9011100
1.7-1.767.10.07927750.9571100
1.76-1.847.10.06427760.9831100
1.84-1.947.10.05127661.1541100
1.94-2.067.10.04327861.1061100
2.06-2.227.10.04427991.12199.9
2.22-2.4570.04728041.1221100
2.45-2.86.90.03728331.0711100
2.8-3.536.80.02528651.077199.9
3.53-506.80.02329530.947198.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→46.673 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.31 / σ(F): 1.34 / Phase error: 14.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1638 2781 5.11 %
Rwork0.136 --
obs0.1374 54382 97.79 %
Solvent computationShrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.31 Å2 / ksol: 0.427 e/Å3
Displacement parametersBiso max: 103.26 Å2 / Biso mean: 21.1063 Å2 / Biso min: 8.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.2752 Å2-0 Å20 Å2
2---1.627 Å2-0 Å2
3---1.3518 Å2
Refinement stepCycle: LAST / Resolution: 1.3→46.673 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1818 0 4 314 2136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091969
X-RAY DIFFRACTIONf_angle_d1.3842674
X-RAY DIFFRACTIONf_chiral_restr0.072282
X-RAY DIFFRACTIONf_plane_restr0.007356
X-RAY DIFFRACTIONf_dihedral_angle_d15.641735
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3-1.32240.33471150.29221942205776
1.3224-1.34650.28091340.24862245237986
1.3465-1.37240.26031270.22192500262796
1.3724-1.40040.21481520.18452586273899
1.4004-1.43080.21051310.153725952726100
1.4308-1.46410.19151400.13826252765100
1.4641-1.50070.171410.124826142755100
1.5007-1.54130.16741390.115226212760100
1.5413-1.58670.15831290.106426152744100
1.5867-1.63790.15521490.100426072756100
1.6379-1.69640.12931460.098426192765100
1.6964-1.76440.13571300.105926472777100
1.7644-1.84470.14281370.110226322769100
1.8447-1.94190.13621370.114626292766100
1.9419-2.06360.14721290.114126572786100
2.0636-2.22290.13361380.120526582796100
2.2229-2.44660.15791410.12626582799100
2.4466-2.80060.15241690.132326592828100
2.8006-3.52830.17031490.136727082857100
3.5283-46.7030.17231480.16322784293298

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