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

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Basic information

Entry
Database: PDB / ID: 3ssh
TitleEngineered high-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 / FOURIER SYNTHESIS / Resolution: 1.277 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
Revision 2.1Oct 16, 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)29,3773
Polymers29,3061
Non-polymers712
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.266, 62.405, 69.325
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: 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 34.99 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 17% PEG3000, 100 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 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: 1.277→41.22 Å / Num. obs: 57869 / % possible obs: 99.5 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.072 / Χ2: 1.216 / Net I/σ(I): 14.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.28-1.35.80.48227981.101198
1.3-1.336.10.43728091.076198.3
1.33-1.356.10.40728551.083198.7
1.35-1.386.10.3627991.096198.5
1.38-1.416.20.30728331.114198.8
1.41-1.446.20.26428761.133198.9
1.44-1.486.20.22928421.183199.3
1.48-1.526.20.19328581.215199.2
1.52-1.566.30.16628831.324199.8
1.56-1.616.40.13628931.317199.9
1.61-1.676.50.11828681.3281100
1.67-1.746.60.10328891.2731100
1.74-1.828.10.1228941.3291100
1.82-1.9113.90.13929181.3791100
1.91-2.0314.20.1129031.2831100
2.03-2.1914.20.09329161.2581100
2.19-2.4114.30.08229411.21100
2.41-2.7614.30.07229541.1521100
2.76-3.4714.10.05929981.1961100
3.47-5013.30.05531421.1131100

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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: 1.277→41.22 Å / Occupancy max: 1 / Occupancy min: 0.27 / SU ML: 0.22 / σ(F): 1.34 / Phase error: 14.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1599 2956 5.12 %
Rwork0.1295 --
obs0.1311 57785 99.01 %
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.3 Å2 / ksol: 0.414 e/Å3
Displacement parametersBiso max: 102.06 Å2 / Biso mean: 19.1446 Å2 / Biso min: 7.06 Å2
Baniso -1Baniso -2Baniso -3
1--5.5314 Å20 Å20 Å2
2--1.2683 Å2-0 Å2
3---4.2631 Å2
Refinement stepCycle: LAST / Resolution: 1.277→41.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1858 0 2 326 2186
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0181961
X-RAY DIFFRACTIONf_angle_d1.7362663
X-RAY DIFFRACTIONf_chiral_restr0.098286
X-RAY DIFFRACTIONf_plane_restr0.011349
X-RAY DIFFRACTIONf_dihedral_angle_d15.388733
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2773-1.29820.23931090.19662331244089
1.2982-1.32060.23931290.18012558268798
1.3206-1.34460.28211420.16582554269699
1.3446-1.37050.20321660.15172548271499
1.3705-1.39850.19621230.12842568269199
1.3985-1.42890.16271400.1262593273399
1.4289-1.46210.17661410.12192581272299
1.4621-1.49870.14221220.11452617273999
1.4987-1.53920.15881310.109626062737100
1.5392-1.58450.14421670.106225812748100
1.5845-1.63570.15191280.100626252753100
1.6357-1.69410.12161390.101526332772100
1.6941-1.76190.1511570.103926132770100
1.7619-1.84210.15171580.110525942752100
1.8421-1.93930.12751400.105926372777100
1.9393-2.06080.1371430.108926382781100
2.0608-2.21990.14361370.115826662803100
2.2199-2.44320.16221330.123726702803100
2.4432-2.79670.1591280.131126942822100
2.7967-3.52330.16151710.140326852856100
3.5233-41.2410.16841520.155728372989100

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