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- PDB-2o29: Spectroscopic and Structural Study of the Heterotropic Linkage be... -

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Entry
Database: PDB / ID: 2o29
TitleSpectroscopic and Structural Study of the Heterotropic Linkage between Halide and Proton Ion Binding to Gfp Proteins: E2(GFP)-BR Complex
ComponentsGreen fluorescent protein
KeywordsLUMINESCENT PROTEIN / LUMINESCENCE / GREEN FLUORESCENT PROTEIN / GFP / E2 / BIOLUMINESCENCE / PHOTOACTIVE PROTEIN / FLUORESCENT CHLORIDE / BROMIDE / IODINE / HALOGEN
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
BROMIDE ION / Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
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.
History
DepositionNov 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_validate_polymer_linkage ...database_2 / pdbx_validate_polymer_linkage / 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 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)27,8385
Polymers27,5181
Non-polymers3204
Water3,207178
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.144, 62.852, 69.172
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Green fluorescent protein


Mass: 27518.010 Da / Num. of mol.: 1 / Mutation: F64L, T203Y, H231L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / References: UniProt: P42212
#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O

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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 Å3/Da / Density % sol: 39.51 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5
Details: 14% (W/V) PEG 3350, 100 MM NH4 ACETATE, 0.2 M NH4Br, PH 5.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 100K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9202
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9202 Å / Relative weight: 1
ReflectionResolution: 1.8→28.684 Å / Num. obs: 20873 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 6.9
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 2 / Rsym value: 0.377 / % possible all: 95.2

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2H6V

2h6v


Resolution: 1.8→15.15 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.926 / SU B: 2.465 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20835 1062 5.1 %RANDOM
Rwork0.17753 ---
obs0.17909 19578 97.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.178 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2---0.75 Å20 Å2
3---0.94 Å2
Refinement stepCycle: LAST / Resolution: 1.8→15.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1885 0 4 179 2068
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221931
X-RAY DIFFRACTIONr_bond_other_d0.0020.021291
X-RAY DIFFRACTIONr_angle_refined_deg1.5231.9672611
X-RAY DIFFRACTIONr_angle_other_deg1.28133172
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8095231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.59125.31296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.55715332
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.815156
X-RAY DIFFRACTIONr_chiral_restr0.0860.2280
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022138
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02376
X-RAY DIFFRACTIONr_nbd_refined0.2620.2326
X-RAY DIFFRACTIONr_nbd_other0.20.21281
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2899
X-RAY DIFFRACTIONr_nbtor_other0.0860.21045
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2930.2116
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3910.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3620.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0671.51490
X-RAY DIFFRACTIONr_mcbond_other0.1711.5474
X-RAY DIFFRACTIONr_mcangle_it1.18121872
X-RAY DIFFRACTIONr_scbond_it2.083908
X-RAY DIFFRACTIONr_scangle_it2.8244.5739
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 80 -
Rwork0.194 1359 -
obs--93.93 %

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