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- PDB-2h9w: Green fluorescent protein ground states: the influence of a secon... -

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Basic information

Entry
Database: PDB / ID: 2h9w
TitleGreen fluorescent protein ground states: the influence of a second protonation site near the chromophore
ComponentsGreen fluorescent protein
KeywordsLUMINESCENT PROTEIN / GFP / CHROMOPHORE / MUTANT / FLUORESCENT / pH / BIOSENSOR / CHLORIDE / HALIDE / 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
Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsGarau, G.
Citation
Journal: Biochemistry / Year: 2007
Title: Green Fluorescent Protein Ground States: The Influence of a Second Protonation Site near the Chromophore.
Authors: Bizzarri, R. / Nifosi, R. / Abbruzzetti, S. / Rocchia, W. / Guidi, S. / Arosio, D. / Garau, G. / Campanini, B. / Grandi, E. / Ricci, F. / Viappiani, C. / Beltram, F.
#1: Journal: To be Published
Title: Spectroscopic and Structural Study of the Heterotropic Linkage between Halide and Proton Ion Binding to Gfp Proteins
Authors: Arosio, D. / Garau, G. / Ricci, F. / Nifosi, R. / Beltram, F.
History
DepositionJun 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Oct 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 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.7Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE THESE COORDINATES USED NON-SEQUENTIAL RESIDUE NUMBERING. MANY NUMBERS WERE SIMPLY SKIPPED ...SEQUENCE THESE COORDINATES USED NON-SEQUENTIAL RESIDUE NUMBERING. MANY NUMBERS WERE SIMPLY SKIPPED IN THE NUMBERING AND HAVE NOTHING TO DO WITH LACK OF ELECTRON DENSITY. Ser 65 was mutated to Thr 65. Thr 65, Tyr 66, and Gly 67 form a chromophore.

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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)27,3283
Polymers27,1361
Non-polymers1922
Water1,964109
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.886, 62.933, 71.035
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: 27135.533 Da / Num. of mol.: 1
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.2 Å3/Da / Density % sol: 42.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: AS, Tris, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979469 / Wavelength: 0.979469 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 1, 2006
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979469 Å / Relative weight: 1
ReflectionResolution: 1.82→47.106 Å / Num. all: 20710 / Num. obs: 20710 / % possible obs: 97.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 8.2
Reflection shellResolution: 1.82→1.92 Å / Redundancy: 3 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.387 / % possible all: 97.2

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CCP4model building
REFMAC5.2.0019refinement
CCP4(SCALA)data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2H6V

2h6v


Resolution: 1.82→47.09 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.189 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.134 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18594 1072 5.2 %RANDOM
Rwork0.16632 ---
obs0.16732 20710 96.33 %-
all-20710 --
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: 19.482 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å20 Å20 Å2
2---0.14 Å20 Å2
3---0.83 Å2
Refinement stepCycle: LAST / Resolution: 1.82→47.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1912 0 10 109 2031
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222011
X-RAY DIFFRACTIONr_bond_other_d0.0020.021329
X-RAY DIFFRACTIONr_angle_refined_deg1.5781.9872720
X-RAY DIFFRACTIONr_angle_other_deg1.38533268
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4025236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.93225.35499
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.29115343
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.754156
X-RAY DIFFRACTIONr_chiral_restr0.0850.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022202
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02389
X-RAY DIFFRACTIONr_nbd_refined0.2760.2307
X-RAY DIFFRACTIONr_nbd_other0.1990.21262
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2926
X-RAY DIFFRACTIONr_nbtor_other0.0860.21128
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.281
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3110.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.215
X-RAY DIFFRACTIONr_mcbond_it1.4281.51512
X-RAY DIFFRACTIONr_mcbond_other0.2021.5486
X-RAY DIFFRACTIONr_mcangle_it1.56121907
X-RAY DIFFRACTIONr_scbond_it2.6453978
X-RAY DIFFRACTIONr_scangle_it3.5254.5813
LS refinement shellResolution: 1.82→1.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 77 -
Rwork0.199 1457 -
obs--97.21 %

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