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- PDB-1emg: GREEN FLUORESCENT PROTEIN (65-67 REPLACED BY CRO, S65T SUBSTITUTI... -

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Basic information

Entry
Database: PDB / ID: 1emg
TitleGREEN FLUORESCENT PROTEIN (65-67 REPLACED BY CRO, S65T SUBSTITUTION, Q80R)
ComponentsPROTEIN (GREEN FLUORESCENT PROTEIN)
KeywordsGREENFLUORESCENT PROTEIN / BIOLUMINESCENCE / PHOTOACTIVE PROTEIN / FLUORESCENT TAG / PH TITRATION
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 Å
AuthorsElsliger, M.A. / Wachter, R.M. / Kallio, K. / Hanson, G.T. / Remington, S.J.
Citation
Journal: Biochemistry / Year: 1999
Title: Structural and spectral response of green fluorescent protein variants to changes in pH.
Authors: Elsliger, M.A. / Wachter, R.M. / Hanson, G.T. / Kallio, K. / Remington, S.J.
#1: Journal: To be Published
Title: Spectral and Structural Response of Gfp Mutants to Variations in Ph and Ionic Strength
Authors: Wachter, R.M. / Elsliger-A, M. / Kallio, K. / Hanson, G.T. / Remington, S.J.
#2: Journal: Structure / Year: 1998
Title: Structural Basis of Spectral Shifts in the Yellow-Emission Variants of Green Fluorescent Protein
Authors: Wachter, R.M. / Elsliger-A, M. / Kallio, K. / Hanson, G.T. / Remington, S.J.
History
DepositionNov 12, 1998Processing site: RCSB
Revision 1.0May 12, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.4Nov 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

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Assembly

Deposited unit
A: PROTEIN (GREEN FLUORESCENT PROTEIN)


Theoretical massNumber of molelcules
Total (without water)26,9451
Polymers26,9451
Non-polymers00
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.733, 62.822, 70.517
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 PROTEIN (GREEN FLUORESCENT PROTEIN)


Mass: 26945.383 Da / Num. of mol.: 1
Mutation: 65 - 67 REPLACED BY CRO, S65T SUBSTITUTION, Q80R SUBSTITUTION
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Strain: JM109(DE3) / Tissue: CIRCUMORAL RING CANAL / Description: THE N-TERMINAL HIS-TAG HAS BEEN REMOVED / Organ: PHOTOGENIC ORGAN / Cellular location (production host): CYTAPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: P42212
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FLUOROPHORE (CRO) IS GENERATED BY AN AUTOCATALYTIC CYCLIZATION OF THE POLYPEPTIDE BACKBONE ...THE FLUOROPHORE (CRO) IS GENERATED BY AN AUTOCATALYTIC CYCLIZATION OF THE POLYPEPTIDE BACKBONE BETWEEN THE NITROGEN OF GLY 67 AND THE CARBONYL CARBON OF THR 65. THE CARBONYL OXYGEN OF THR 65 LEAVES AS WATER, AND IS NOT PRESENT IN THE MODEL. A SUBSEQUENT OXIDATION OF THE CA - CB BOND OF TYR 66 LINKS THE CONJUGATED SYSTEM OF THE TYROSINE RING TO THAT OF THE FORMED BACKBONE IMIDAZOLIDINONE. RESIDUES 65, 66, AND 67 ARE NOT PRESENT IN THE ENTRY AND ARE INSTEAD REPLACED WITH CRO 66.

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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: 2.1 Å3/Da / Density % sol: 42.17 %
Crystal growpH: 8
Details: CRYSTALLIZATION CONDITIONS: 22-26% PEG 4000, 50 MM HEPES PH 8.0, 50 MM MGCL2, 12 MG PROTEIN
Crystal grow
*PLUS
pH: 7.9 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlprotein1drop
220 mMTris1drop
350 mMHEPES1reservoir
450 mM1reservoirMgCl2
523-26 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 16011 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.075
Reflection shellResolution: 2→2.05 Å / % possible all: 94
Reflection
*PLUS
Num. measured all: 93073
Reflection shell
*PLUS
% possible obs: 94 %

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Processing

Software
NameClassification
TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling
TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EMA

1ema


Resolution: 2→20 Å / Isotropic thermal model: TNT / Stereochemistry target values: TNT
RfactorNum. reflection% reflection
Rwork0.186 --
obs-16011 99 %
Solvent computationSolvent model: BABINET SCALING / Bsol: 148.1 Å2 / ksol: 0.769 e/Å3
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1737 0 0 99 1836
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00918170.8
X-RAY DIFFRACTIONt_angle_deg2.124561.3
X-RAY DIFFRACTIONt_dihedral_angle_d19.1810510
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.005472
X-RAY DIFFRACTIONt_gen_planes0.0122655
X-RAY DIFFRACTIONt_it3.7218101
X-RAY DIFFRACTIONt_nbd0.023910
Software
*PLUS
Name: TNT / Version: 5F / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_angle_deg2.1
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg19.180
X-RAY DIFFRACTIONt_planar_d0.0052
X-RAY DIFFRACTIONt_plane_restr0.0125

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