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- PDB-1eme: GREEN FLUORESCENT PROTEIN FROM AEQUOREA VICTORIA, MUTANT -

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Basic information

Entry
Database: PDB / ID: 1eme
TitleGREEN FLUORESCENT PROTEIN FROM AEQUOREA VICTORIA, MUTANT
ComponentsGREEN FLUORESCENT PROTEIN
KeywordsLUMINESCENCE / FLUORESCENT PROTEIN / BETA-BARREL / BIOLUMINESCENCE
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: 2.5 Å
AuthorsPalm, G. / Zdanov, A. / Wlodawer, A.
CitationJournal: Nat.Struct.Biol. / Year: 1997
Title: The structural basis for spectral variations in green fluorescent protein.
Authors: Palm, G.J. / Zdanov, A. / Gaitanaris, G.A. / Stauber, R. / Pavlakis, G.N. / Wlodawer, A.
History
DepositionMar 31, 1997Processing site: BNL
Revision 1.0Aug 20, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 21, 2015Group: Structure summary
Revision 2.0Nov 3, 2021Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Other
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_database_status / struct_conn / struct_ref_seq_dif
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.1Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 3.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_close_contact / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.ptnr1_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GREEN FLUORESCENT PROTEIN


Theoretical massNumber of molelcules
Total (without water)26,9411
Polymers26,9411
Non-polymers00
Water1,33374
1
A: GREEN FLUORESCENT PROTEIN

A: GREEN FLUORESCENT PROTEIN


Theoretical massNumber of molelcules
Total (without water)53,8832
Polymers53,8832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation46_455z-1/4,-y+3/4,x+1/41
Unit cell
Length a, b, c (Å)175.600, 175.600, 175.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132
Components on special symmetry positions
IDModelComponents
11A-601-

HOH

21A-602-

HOH

31A-603-

HOH

41A-604-

HOH

DetailsTHE BIOLOGICALLY ACTIVE MOLECULE IS A DIMER.

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Components

#1: Protein GREEN FLUORESCENT PROTEIN / / GFP


Mass: 26941.283 Da / Num. of mol.: 1 / Mutation: INS(A1[B]), F64L, I167T, K238N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Tissue: CIRCUMORAL RING CANAL / Gene: GFP / Organ: PHOTOGENIC ORGAN / Plasmid: PFRED11 / Cellular location (production host): CYTOPLASM / Gene (production host): SG11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21, OMEGA800 / References: UniProt: P42212
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsGYS 66: THE CHROMOPHORE IS PART OF THE PEPTIDE CHAIN BETWEEN RESIDUES 64 AND 68.

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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: 4.2 Å3/Da / Density % sol: 71 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.5
Details: PROTEIN WAS CRYSTALLIZED BY HANGING DROP METHOD. PROTEIN SOLUTION: 13 MG/ML IN 20 MM TRIS/HCL WELL SOLUTION: 1.8 M AS, 100 MM TRIS/HCL, PH 8.5 PROTEIN:WELL 1:1, vapor diffusion - hanging drop
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: protein solution is mixed in a 1:1 ratio with well solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
113 mg/mlprotein1drop
220 mMTris-HCl1drop
31.8 Mammonium sulfate1reservoir
4100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MAC Science DIP-2000 / Detector: IMAGE PLATE / Date: Mar 5, 1996 / Details: MIRROR
RadiationMonochromator: NI / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 15816 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 9.4 % / Rsym value: 0.145 / Net I/σ(I): 6.5
Reflection shellResolution: 2.5→2.54 Å / Mean I/σ(I) obs: 2.9 / Rsym value: 0.291 / % possible all: 94.7
Reflection
*PLUS
Rmerge(I) obs: 0.094
Reflection shell
*PLUS
% possible obs: 94.7 % / Rmerge(I) obs: 0.291

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EMA

1ema


Resolution: 2.5→10 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: PARAMETERS FOR THE CHROMOPHORE WERE ESTIMATED ACCORDING TO A MODEL COMPOUND (B.TINANT ET AL., CRYST. STRUCT. COMM., 1980, 9, 671-674)
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1006 7 %RANDOM
Rwork0.198 ---
obs0.198 15152 94.9 %-
Displacement parametersBiso mean: 14.3 Å2
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1788 0 0 74 1862
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.019
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.154
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.93
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.006
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.331.5
X-RAY DIFFRACTIONx_mcangle_it1.172
X-RAY DIFFRACTIONx_scbond_it1.332
X-RAY DIFFRACTIONx_scangle_it1.172.5
LS refinement shellResolution: 2.5→2.61 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.389 104 5.2 %
Rwork0.291 1760 -
obs--88.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PAR_CSY.PROTOP_CSY.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.93
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.006
LS refinement shell
*PLUS
Rfactor obs: 0.291

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