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

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Basic information

Entry
Database: PDB / ID: 1eml
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: 2.3 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 1.4Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details
Revision 1.5Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.0Nov 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 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.ptnr1_label_atom_id
Revision 2.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)26,9411
Polymers26,9411
Non-polymers00
Water1,892105
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 operation11_555-x+y,y,-z+1/21
Unit cell
Length a, b, c (Å)89.700, 89.700, 130.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsTHE AUTHOR NOTED THAT THE 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, 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


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.8 Å3/Da / Density % sol: 57 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.5
Details: PROTEIN WAS CRYSTALLIZED BY HANGING DROP METHOD. PROTEIN SOLUTION: 17 MG/ML IN 20 MM TRISCL WELL SOLUTION: 2.0 M AS, 100 MM TRISCL, PH 8.5 (HAMPTON SCREEN I, SOLUTION 4) PROTEIN:WELL 1:1, ...Details: PROTEIN WAS CRYSTALLIZED BY HANGING DROP METHOD. PROTEIN SOLUTION: 17 MG/ML IN 20 MM TRISCL WELL SOLUTION: 2.0 M AS, 100 MM TRISCL, PH 8.5 (HAMPTON SCREEN I, SOLUTION 4) PROTEIN:WELL 1:1, vapor diffusion - hanging drop
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
113-22 mg/mlprotein1drop
21.8-2.2 Mammonium sulfate1reservoir
3100 mMTrisSO41reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 20, 1996 / Details: MIRROR
RadiationMonochromator: NI / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 14046 / % possible obs: 97.6 % / Observed criterion σ(I): 1 / Redundancy: 7.8 % / Rsym value: 0.102
Reflection shellResolution: 2.3→2.4 Å / % possible all: 87.8
Reflection
*PLUS
Rmerge(I) obs: 0.102
Reflection shell
*PLUS
% possible obs: 87.8 %

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Processing

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

1ema


Resolution: 2.3→10 Å / Rfactor Rfree error: 0.0086 / 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
Rfree0.285 916 7 %RANDOM
Rwork0.201 ---
obs0.201 13793 97.6 %-
Displacement parametersBiso mean: 30.2 Å2
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1750 0 0 105 1855
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d
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_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.124
X-RAY DIFFRACTIONx_mcangle_it1.225
X-RAY DIFFRACTIONx_scbond_it1.124.5
X-RAY DIFFRACTIONx_scangle_it1.225.5
LS refinement shellResolution: 2.3→2.4 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.339 102 5.97 %
Rwork0.271 1500 -
obs--93.7 %
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
LS refinement shell
*PLUS
Rfactor obs: 0.271

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