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- PDB-8dta: Metal sensitive GFP (mseGFP) complexed with phenylarsine oxide. -

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Basic information

Entry
Database: PDB / ID: 8dta
TitleMetal sensitive GFP (mseGFP) complexed with phenylarsine oxide.
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / GFP / PAO / ARSENIC
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / Phenylarsine oxide / DI(HYDROXYETHYL)ETHER / Green fluorescent protein
Function and homology information
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsRosenbaum, J.C. / Carlson, A.E.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
Citation
Journal: TBD
Title: Glutathione modulates metal binding to proteins.
Authors: Rosenbaum, J.C. / Carlson, A.E.
#1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
History
DepositionJul 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 2.0Jan 31, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_contact_author / pdbx_poly_seq_scheme / pdbx_struct_assembly_prop / pdbx_unobs_or_zero_occ_residues / refine / refine_ls_restr / refine_ls_shell / software / struct_conn / struct_ref / struct_ref_seq_dif
Item: _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code ..._entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine_ls_restr.dev_ideal / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _struct_conn.pdbx_dist_value / _struct_ref.pdbx_align_begin
Description: Ligand geometry
Details: I submitted -- in my haste -- a previous refinement where I had not yet completed my adjustment of the ligand position. The only difference is the ligand position plus some IBF/occupancy ...Details: I submitted -- in my haste -- a previous refinement where I had not yet completed my adjustment of the ligand position. The only difference is the ligand position plus some IBF/occupancy refinements. But all other coordinates are identical
Provider: author / Type: Coordinate replacement

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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)27,7427
Polymers27,1301
Non-polymers6126
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy, Metal binding was typically assessed by a ratiometric change in fluorescence in a plate reader and by fluorescence microscopy.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-22 kcal/mol
Surface area11780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.802, 126.802, 126.802
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Space group name HallI223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1/2,x+1/2
#17: z+1/2,-x+1/2,-y+1/2
#18: -y+1/2,z+1/2,-x+1/2
#19: -z+1/2,-x+1/2,y+1/2
#20: -z+1/2,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1/2
#22: x+1/2,-y+1/2,-z+1/2
#23: -x+1/2,y+1/2,-z+1/2
#24: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-407-

HOH

21A-624-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Green fluorescent protein


Mass: 27129.701 Da / Num. of mol.: 1 / Mutation: C48S,F64L,S147C,S202C,H231L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P42212

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Non-polymers , 5 types, 256 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PA0 / Phenylarsine oxide / oxo(phenyl)arsane


Mass: 168.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5AsO / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.13 Å3/Da / Density % sol: 60.8 % / Description: Cubic
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1M Tris, pH 8 0.2M Lithium sulfate 32% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: NITROGEN STREAM / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jul 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.81→33.9 Å / Num. obs: 30947 / % possible obs: 99.71 % / Redundancy: 17.5 % / Biso Wilson estimate: 23.4 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1114 / Rpim(I) all: 0.02724 / Rrim(I) all: 0.1148 / Net I/σ(I): 33.07
Reflection shellResolution: 1.81→1.875 Å / Redundancy: 17.4 % / Rmerge(I) obs: 1.018 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 3068 / CC1/2: 0.85 / CC star: 0.959 / Rpim(I) all: 0.25 / Rrim(I) all: 1.049 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASER1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JC0

1jc0


Resolution: 1.81→33.89 Å / SU ML: 0.1819 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.8774
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.183 1989 6.44 %Random
Rwork0.1641 28877 --
obs0.1653 30866 99.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.23 Å2
Refinement stepCycle: LAST / Resolution: 1.81→33.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1887 0 32 250 2169
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01331960
X-RAY DIFFRACTIONf_angle_d1.25142642
X-RAY DIFFRACTIONf_chiral_restr0.0662281
X-RAY DIFFRACTIONf_plane_restr0.0113343
X-RAY DIFFRACTIONf_dihedral_angle_d15.476734
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.860.27221420.21592046X-RAY DIFFRACTION100
1.86-1.910.26031430.22712042X-RAY DIFFRACTION99.73
1.91-1.960.28731400.23832044X-RAY DIFFRACTION99.23
1.96-2.030.20421430.17732027X-RAY DIFFRACTION100
2.03-2.10.2461430.20392063X-RAY DIFFRACTION99.77
2.1-2.180.18341400.15142045X-RAY DIFFRACTION100
2.18-2.280.21341360.19692033X-RAY DIFFRACTION98.32
2.28-2.40.18471420.15672048X-RAY DIFFRACTION100
2.4-2.550.1761440.15812070X-RAY DIFFRACTION100
2.55-2.750.17341400.15882058X-RAY DIFFRACTION99.95
2.75-3.020.18941400.16982074X-RAY DIFFRACTION99.91
3.03-3.460.18361400.15252085X-RAY DIFFRACTION99.87
3.47-4.360.13441450.13342097X-RAY DIFFRACTION99.78
4.36-33.890.16651510.16142145X-RAY DIFFRACTION99.74

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