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- PDB-2o24: Spectroscopic and Structural Study of the Heterotropic Linkage be... -

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Basic information

Entry
Database: PDB / ID: 2o24
TitleSpectroscopic and Structural Study of the Heterotropic Linkage between Halide and Proton Ion Binding to Gfp Proteins: E2(GFP)-Cl Complex
ComponentsGreen fluorescent protein
KeywordsLUMINESCENT PROTEIN / LUMINESCENCE / GREEN FLUORESCENT PROTEIN / GFP / E2 / BIOLUMINESCENCE / PHOTOACTIVE PROTEIN / FLUORESCENT CHLORIDE / BROMIDE / IODINE / HALOGEN
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / protein-chromophore linkage / Green fluorescent protein
Function and homology information
Specimen sourceAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 1.45 Å resolution
AuthorsGarau, G.
CitationJournal: Biophys.J. / Year: 2007
Title: Spectroscopic and Structural Study of Proton and Halide Ion Cooperative Binding to GFP.
Authors: Arosio, D. / Garau, G. / Ricci, F. / Marchetti, L. / Bizzarri, R. / Beltram, F.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 29, 2006 / Release: May 15, 2007
RevisionDateData content typeGroupProviderType
1.0May 15, 2007Structure modelrepositoryInitial release
1.1May 1, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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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)27,6244
Polyers27,5181
Non-polymers1063
Water3,837213
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)50.989, 62.979, 69.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21

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Components

#1: Protein/peptide Green fluorescent protein /


Mass: 27518.010 Da / Num. of mol.: 1 / Mutation: F64L, T203Y, H231L / Source: (gene. exp.) Aequorea victoria (jellyfish) / Genus: Aequorea / Gene: GFP / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: P42212
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Formula: Cl / Chloride
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Formula: H2O / Water

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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: 2.03 / Density percent sol: 39.51 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5
Details: 14% (W/V) PEG 3350, 100 MM NH4 ACETATE, 0.2 M NH4CL, PH 5.0, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 1 kelvins
SourceSource: SYNCHROTRON / Type: ESRF BEAMLINE ID14-1 / Synchrotron site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorDetector: CCD
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionD resolution high: 1.45 Å / D resolution low: 28.684 Å / Number obs: 38294 / Observed criterion sigma I: 2 / Rmerge I obs: 0.074 / Rsym value: 0.074 / NetI over sigmaI: 5.8 / Redundancy: 7.1 % / Percent possible obs: 97
Reflection shellRmerge I obs: 0.338 / Highest resolution: 1.45 Å / Lowest resolution: 1.53 Å / MeanI over sigI obs: 2.2 / Rsym value: 0.338 / Redundancy: 6.8 % / Percent possible all: 95.8

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0019refinement
ADSCdata collection
MOSFLMdata reduction
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2H6V
Correlation coeff Fo to Fc: 0.957 / Correlation coeff Fo to Fc free: 0.949 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS / Overall SU B: 1.004 / Overall SU ML: 0.04 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Overall ESU R: 0.073 / Overall ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Solvent computationSolvent ion probe radii: 0.8 Å / Solvent shrinkage radii: 0.8 Å / Solvent vdw probe radii: 1.2 Å / Solvent model details: BABINET MODEL WITH MASK
Displacement parametersB iso mean: 12.127 Å2 / Aniso B11: -0.02 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: -0.39 Å2 / Aniso B23: 0 Å2 / Aniso B33: 0.41 Å2
Least-squares processR factor R free: 0.19157 / R factor R work: 0.17732 / R factor obs: 0.17805 / Highest resolution: 1.45 Å / Lowest resolution: 28.68 Å / Number reflection R free: 1951 / Number reflection obs: 36954 / Percent reflection R free: 5 / Percent reflection obs: 96.52
Refine hist #LASTHighest resolution: 1.45 Å / Lowest resolution: 28.68 Å
Number of atoms included #LASTProtein: 1911 / Nucleic acid: 0 / Ligand: 3 / Solvent: 217 / Total: 2131
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221957
X-RAY DIFFRACTIONr_bond_other_d0.0020.0201304
X-RAY DIFFRACTIONr_angle_refined_deg1.4001.9692645
X-RAY DIFFRACTIONr_angle_other_deg1.5183.0003205
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5275.000233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.91425.25897
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.13715.000336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.13315.0006
X-RAY DIFFRACTIONr_chiral_restr0.0740.200284
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0202160
X-RAY DIFFRACTIONr_gen_planes_other0.0010.020382
X-RAY DIFFRACTIONr_nbd_refined0.2620.200302
X-RAY DIFFRACTIONr_nbd_other0.1980.2001277
X-RAY DIFFRACTIONr_nbtor_refined0.1750.200915
X-RAY DIFFRACTIONr_nbtor_other0.0880.2001064
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2730.200128
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1530.20017
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2390.20043
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.20036
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7841.5001239
X-RAY DIFFRACTIONr_mcbond_other0.1351.500480
X-RAY DIFFRACTIONr_mcangle_it1.1212.0001892
X-RAY DIFFRACTIONr_scbond_it1.7893.000863
X-RAY DIFFRACTIONr_scangle_it2.4724.500753
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS shellHighest resolution: 1.45 Å / R factor R free: 0.222 / R factor R work: 0.196 / Lowest resolution: 1.488 Å / Number reflection R free: 155 / Number reflection R work: 2625 / Total number of bins used: 20 / Percent reflection obs: 95.27

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