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- PDB-1gfl: STRUCTURE OF GREEN FLUORESCENT PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1gfl
TitleSTRUCTURE OF GREEN FLUORESCENT PROTEIN
ComponentsGREEN FLUORESCENT PROTEIN
KeywordsFLUORESCENT PROTEIN / FLUOROPHORE GREEN FLUORESCENT PROTEIN / LUMINESCENCE
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 / Resolution: 1.9 Å
AuthorsYang, F. / Moss, L.G. / Phillips Jr., G.N.
Citation
Journal: Nat.Biotechnol. / Year: 1996
Title: The molecular structure of green fluorescent protein.
Authors: Yang, F. / Moss, L.G. / Phillips Jr., G.N.
#1: Journal: Trends Biochem.Sci. / Year: 1995
Title: Understanding, Improving and Using Green Fluorescent Proteins
Authors: Cubitt, A.B. / Heim, R. / Adams, S.R. / Boyd, A.E. / Gross, L.A. / Tsien, R.Y.
History
DepositionAug 23, 1996Processing site: BNL
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 24, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_assembly / pdbx_struct_assembly_gen / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
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:
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Assembly

Deposited unit
A: GREEN FLUORESCENT PROTEIN
B: GREEN FLUORESCENT PROTEIN


Theoretical massNumber of molelcules
Total (without water)53,7832
Polymers53,7832
Non-polymers00
Water5,405300
1
A: GREEN FLUORESCENT PROTEIN


Theoretical massNumber of molelcules
Total (without water)26,8911
Polymers26,8911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GREEN FLUORESCENT PROTEIN


Theoretical massNumber of molelcules
Total (without water)26,8911
Polymers26,8911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.226, 89.226, 119.771
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.950278, 0.287772, 0.118992), (0.294841, 0.708504, 0.641164), (0.100202, 0.644367, -0.758123)
Vector: 7.36697, 13.04218, -38.10565)

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Components

#1: Protein GREEN FLUORESCENT PROTEIN


Mass: 26891.271 Da / Num. of mol.: 2 / Mutation: Q80R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Plasmid: PTU58 / Production host: Escherichia coli (E. coli) / References: UniProt: P42212
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE FLUOROPHORE IS FORMED BY SER 65, TYR 66 AND GLY 67. THE CARBONYL CARBON OF TYR 66 IS BONDED TO ...THE FLUOROPHORE IS FORMED BY SER 65, TYR 66 AND GLY 67. THE CARBONYL CARBON OF TYR 66 IS BONDED TO THE NITROGEN OF GLY 67. THE CARBONYL OXYGEN IS DELETED. THE SIDE CHAIN OF TYR 66 IS DEHYDROGENATED.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.48 %
Crystal growpH: 7 / Details: FREE TEXT GOES HERE., pH 7.0

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Data collection

DiffractionMean temperature: 299 K
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Mar 25, 1995
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 38472 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.077

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementResolution: 1.9→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.262 --
Rwork0.214 --
obs0.214 37225 96.8 %
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3650 0 0 300 3950
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg1.79
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d29.47
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.386
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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