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- PDB-1rrx: Crystallographic Evidence for Isomeric Chromophores in 3-Fluoroty... -

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Basic information

Entry
Database: PDB / ID: 1rrx
TitleCrystallographic Evidence for Isomeric Chromophores in 3-Fluorotyrosyl-Green Fluorescent Protein
ComponentsSIGF1-GFP fusion protein
KeywordsLUMINESCENT PROTEIN / Beta-barrel / EGFP / Non-canonical amino acid / chromophore isomerisation
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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBae, J.H. / Paramita Pal, P. / Moroder, L. / Huber, R. / Budisa, N.
CitationJournal: Chembiochem / Year: 2004
Title: Crystallographic Evidence for Isomeric Chromophores in 3-Fluorotyrosyl-Green Fluorescent Protein.
Authors: Bae, J.H. / Paramita Pal, P. / Moroder, L. / Huber, R. / Budisa, N.
History
DepositionDec 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_polymer_linkage / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / struct_conn / struct_ref_seq_dif
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_polymer_linkage.auth_atom_id_1 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SIGF1-GFP fusion protein


Theoretical massNumber of molelcules
Total (without water)25,8541
Polymers25,8541
Non-polymers00
Water1,09961
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.003, 62.430, 70.931
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein SIGF1-GFP fusion protein


Mass: 25853.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: contains 3-fluoro-tyrosine / Source: (gene. exp.) Aequorea victoria (jellyfish) / Production host: Escherichia coli (E. coli) / References: UniProt: P42212
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.18 Å3/Da / Density % sol: 43.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 12, 2003
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 13748 / Num. obs: 13596 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Biso Wilson estimate: 14.6 Å2
Reflection shellResolution: 2.1→2.18 Å / % possible all: 96.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→41.41 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 538144.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1311 10 %RANDOM
Rwork0.225 ---
obs0.2251 13067 94.9 %-
all-13748 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.1979 Å2 / ksol: 0.385028 e/Å3
Displacement parametersBiso mean: 22.8 Å2
Baniso -1Baniso -2Baniso -3
1--4.5 Å20 Å20 Å2
2---2.77 Å20 Å2
3---7.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.1→41.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1820 0 0 61 1881
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006665
X-RAY DIFFRACTIONc_angle_deg1.42684
X-RAY DIFFRACTIONc_dihedral_angle_d32.6
X-RAY DIFFRACTIONc_improper_angle_d14.21
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.317 174 8.6 %
Rwork0.245 1846 -
obs--89.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION2PRO_MFPRO_MF
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP

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