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

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Basic information

Entry
Database: PDB / ID: 3svc
TitleEngineered medium-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: 1.31 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 2.1Nov 20, 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)29,4765
Polymers29,3081
Non-polymers1684
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.615, 62.664, 65.951
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: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 303 / 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: 1.82 Å3/Da / Density % sol: 32.4 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 20% PEG2000, 50 mM sodium acetate, 90 mM magnesium chloride, pH 4.6, 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: 1.1169 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 11, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1169 Å / Relative weight: 1
ReflectionResolution: 1.31→50 Å / Num. obs: 51271 / % possible obs: 98.3 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.049 / Χ2: 1.03 / Net I/σ(I): 16
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.31-1.336.10.48624870.952197.8
1.33-1.366.60.42725400.892197.8
1.36-1.386.60.37225210.922198.9
1.38-1.416.60.30925300.943198.4
1.41-1.446.60.25525280.955198.3
1.44-1.486.60.20925700.973198.5
1.48-1.516.70.16925301.01199.2
1.51-1.556.70.13825571.017199.1
1.55-1.66.80.11225611.075199.2
1.6-1.656.90.09325811.164199.3
1.65-1.716.90.0825641.179199.5
1.71-1.7870.07125981.219199.5
1.78-1.8670.0625901.056199.6
1.86-1.966.90.05325761.132199.8
1.96-2.086.90.05226101.045199.4
2.08-2.246.80.05326061.142199.5
2.24-2.476.70.04726341.072199.4
2.47-2.826.50.03926160.89199.3
2.82-3.566.70.03326400.943198.4
3.56-506.20.03324320.941185.9

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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
Starting model: PDB ENTRY 3SST

3sst


Resolution: 1.31→39.84 Å / Occupancy max: 1 / Occupancy min: 0.27 / SU ML: 0.31 / σ(F): 1.35 / Phase error: 13.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1643 2612 5.1 %
Rwork0.134 --
obs0.1356 51213 98.21 %
Solvent computationShrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.639 Å2 / ksol: 0.473 e/Å3
Displacement parametersBiso max: 99.54 Å2 / Biso mean: 20.6598 Å2 / Biso min: 7.32 Å2
Baniso -1Baniso -2Baniso -3
1-1.6479 Å20 Å2-0 Å2
2--0.2437 Å20 Å2
3----1.8916 Å2
Refinement stepCycle: LAST / Resolution: 1.31→39.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1841 0 7 303 2151
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091974
X-RAY DIFFRACTIONf_angle_d1.3072680
X-RAY DIFFRACTIONf_chiral_restr0.072285
X-RAY DIFFRACTIONf_plane_restr0.007355
X-RAY DIFFRACTIONf_dihedral_angle_d14.735733
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3097-1.33350.33291450.3052433257896
1.3335-1.35910.32251200.25792555267598
1.3591-1.38690.24991470.21522485263299
1.3869-1.4170.24561420.1772550269299
1.417-1.450.21851390.14832538267798
1.45-1.48630.16911280.12072523265199
1.4863-1.52650.16711390.10972579271899
1.5265-1.57140.16541370.09732549268699
1.5714-1.62210.13861440.09532557270199
1.6221-1.68010.15991190.096625882707100
1.6801-1.74730.15071460.097325772723100
1.7473-1.82690.1461300.106725932723100
1.8269-1.92320.13431300.106925812711100
1.9232-2.04370.14311340.112226042738100
2.0437-2.20140.14371480.114726002748100
2.2014-2.4230.13221240.11662631275599
2.423-2.77350.13961640.13052595275999
2.7735-3.4940.16461450.1352656280199
3.494-39.85870.18471310.17762407253886

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