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- PDB-1ema: GREEN FLUORESCENT PROTEIN FROM AEQUOREA VICTORIA -

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Basic information

Entry
Database: PDB / ID: 1ema
TitleGREEN FLUORESCENT PROTEIN FROM AEQUOREA VICTORIA
ComponentsGREEN FLUORESCENT PROTEIN
KeywordsFLUORESCENT PROTEIN / BETA-BARREL / AUTOCATALYTIC / FLUOROPHORE / BIOLUMINESCENSE FLUORESCENT PROTEIN
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 / MIR/SAD / Resolution: 1.9 Å
AuthorsOrmo, M. / Remington, S.J.
Citation
Journal: Science / Year: 1996
Title: Crystal structure of the Aequorea victoria green fluorescent protein.
Authors: Ormo, M. / Cubitt, A.B. / Kallio, K. / Gross, L.A. / Tsien, R.Y. / Remington, S.J.
#1: Journal: Nature / Year: 1995
Title: Improved Green Fluorescence
Authors: Heim, R. / Cubitt, A.B. / Tsien, R.Y.
History
DepositionAug 1, 1996Processing site: BNL
Revision 1.0Nov 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _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 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GREEN FLUORESCENT PROTEIN


Theoretical massNumber of molelcules
Total (without water)27,2271
Polymers27,2271
Non-polymers00
Water1,71195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.770, 62.850, 70.670
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: 27226.754 Da / Num. of mol.: 1 / Mutation: 65 - 67 REPLACED BY CRO, Q80R
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN CONTAINS SIX SE-METHIONINES. OF THESE, THE N-TERMINAL MET AND MET 233 ARE NOT PRESENT IN THE ENTRY
Source: (gene. exp.) Aequorea victoria (jellyfish) / Description: THE N-TERMINAL HIS-TAG HAS BEEN REMOVED / Organ: LEAVES / Plasmid: PRSETB (INVITROGEN) / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 (DE3) / References: UniProt: P42212
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 40.5 %
Crystal growpH: 8.2
Details: 22-26% PEG 4000, 50 MM HEPES PH 8.0-8.4, 50 MM MGCL2, 10 MM 2-MERCAPTOETHANOL, 5-7 MG PROTEIN, pH 8.2
PH range: 8.0-8.4
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
122-26 %PEG40001reservoir
250 mMHEPES1reservoir
350 mM1reservoirMgCl2
410 mM2-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Apr 28, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionHighest resolution: 1.9 Å / Num. obs: 17676 / % possible obs: 84 % / Observed criterion σ(I): 0 / Redundancy: 6.45 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.09

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Processing

Software
NameVersionClassification
CCP4model building
PROTEINmodel building
TNT5-Frefinement
HKLdata reduction
HKLdata scaling
CCP4phasing
PROTEINphasing
RefinementMethod to determine structure: MIR/SAD / Resolution: 1.9→20 Å / Isotropic thermal model: TNT / σ(F): 0 / Stereochemistry target values: TNT
Details: THE FINAL (FO-FC) DENSITY SHOWS LARGE DIFFERENCE FEATURES LOCATED AROUND THE MAIN CHAIN PART OF THE FLUOROPHORE THAT ORIGINATES FROM RESIDUES THR 65 AND GLY 67. THE DIFFERENCE DENSITIES ALSO ...Details: THE FINAL (FO-FC) DENSITY SHOWS LARGE DIFFERENCE FEATURES LOCATED AROUND THE MAIN CHAIN PART OF THE FLUOROPHORE THAT ORIGINATES FROM RESIDUES THR 65 AND GLY 67. THE DIFFERENCE DENSITIES ALSO AFFECT THE ATOMIC-POSITION REFINEMENT OF VAL 68. THE DIFFERENCE FEATURES MIGHT BE EXPLAINED AS A SUBSET (<30%) OF MOLECULES THAT HAS FAILED TO UNDERGO THE COMPLETE FORMATION OF THE FLUOROPHORE. THE LOOP RESIDUES 157 AND 158 ARE DISORDERED. A NUMBER OF SURFACE RESIDUES HAVE TRUNCATED SIDE CHAINS DUE TO WEAK OR NO DENSITY.
Num. reflection% reflection
obs17676 84 %
Solvent computationSolvent model: BABINET SCALING / Bsol: 300 Å2 / ksol: 0.8 e/Å3
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1771 0 0 95 1866
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01418151.3
X-RAY DIFFRACTIONt_angle_deg1.9524534.4
X-RAY DIFFRACTIONt_dihedral_angle_d19.6510500
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.014472
X-RAY DIFFRACTIONt_gen_planes0.0182648.5
X-RAY DIFFRACTIONt_it4.2917712.4
X-RAY DIFFRACTIONt_nbd0.0411310
Software
*PLUS
Name: TNT / Version: 5-F / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.175
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 24.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg19.650
X-RAY DIFFRACTIONt_plane_restr0.018

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