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- PDB-1yfp: STRUCTURE OF YELLOW-EMISSION VARIANT OF GFP -

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Basic information

Entry
Database: PDB / ID: 1yfp
TitleSTRUCTURE OF YELLOW-EMISSION VARIANT OF GFP
ComponentsYELLOW FLUORESCENT PROTEIN
KeywordsLUMINESCENCE / GREEN FLUORESCENT PROTEIN / YELLOW-EMISSION VARIANT / BIOLUMINESCENCE / PHOTOACTIVE PROTEIN / FLUORESCENT TAG
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
AuthorsWachter, R.M. / Elsliger, M.-A. / Kallio, K. / Hanson, G.T. / Remington, S.J.
CitationJournal: Structure / Year: 1998
Title: Structural basis of spectral shifts in the yellow-emission variants of green fluorescent protein.
Authors: Wachter, R.M. / Elsliger, M.A. / Kallio, K. / Hanson, G.T. / Remington, S.J.
History
DepositionAug 28, 1998Processing site: BNL
Revision 1.0Oct 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 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_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 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 999THE CHROMOPHORE CRO IS GENERATED BY AN AUTOCATALYTIC CYCLIZATION OF THE POLYPEPTIDE BACKBONE OF SER ...THE CHROMOPHORE CRO IS GENERATED BY AN AUTOCATALYTIC CYCLIZATION OF THE POLYPEPTIDE BACKBONE OF SER 65, TYR 66, GLY 67. RESIDUES SER65 under went mutation to GLY65 before cyclization.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YELLOW FLUORESCENT PROTEIN
B: YELLOW FLUORESCENT PROTEIN


Theoretical massNumber of molelcules
Total (without water)51,4202
Polymers51,4202
Non-polymers00
Water1,838102
1
A: YELLOW FLUORESCENT PROTEIN


Theoretical massNumber of molelcules
Total (without water)25,7101
Polymers25,7101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YELLOW FLUORESCENT PROTEIN


Theoretical massNumber of molelcules
Total (without water)25,7101
Polymers25,7101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.308, 117.655, 62.919
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99998, -0.00309, -0.00619), (-0.00319, -0.58661, 0.80986), (-0.00613, 0.80986, 0.58659)
Vector: 98.2064, 21.138, -10.7766)

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Components

#1: Protein YELLOW FLUORESCENT PROTEIN


Mass: 25709.994 Da / Num. of mol.: 2 / Mutation: S65G, V68L, S72A, Q80R, H148G, T203Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Tissue: CIRCUMORAL RING CANAL / Gene: GFP / Organ: PHOTOGENIC ORGAN / Plasmid: PRSETB (INVITROGEN) / Cellular location (production host): CYTOPLASM / 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.: 102 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.4 % / Description: ISOMORPHOUS REPLACEMENT
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: YFP WAS CONCENTRATED TO 10 MG/ML IN 50 MM HEPES PH 7.5. ROD-SHAPED CRYSTALS WITH APPROXIMATE DIMENSIONS OF 0.8 X 0.12 X 0.03 MM WERE GROWN IN HANGING DROPS CONTAINING 5 MICROLITERS PROTEIN ...Details: YFP WAS CONCENTRATED TO 10 MG/ML IN 50 MM HEPES PH 7.5. ROD-SHAPED CRYSTALS WITH APPROXIMATE DIMENSIONS OF 0.8 X 0.12 X 0.03 MM WERE GROWN IN HANGING DROPS CONTAINING 5 MICROLITERS PROTEIN AND 5 MICROLITERS MOTHER LIQUOR AT 15 DEGREES C AFTER 2 WEEKS. THE MOTHER LIQUOR CONTAINED 2.2 M SODIUM/POTASSIUM PHOSPHATE PH 6.9., vapor diffusion - hanging drop, temperature 288K
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 15 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
250 mMHEPES1drop
32.2 Msodium potassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Dec 5, 1997 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 18916 / % possible obs: 92 % / Observed criterion σ(I): 1.9 / Redundancy: 4 % / Biso Wilson estimate: 28.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.8
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 4 % / % possible all: 94
Reflection
*PLUS
Num. measured all: 53039 / Rmerge(I) obs: 0.08
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: 2.5→20 Å / Isotropic thermal model: TNT / Stereochemistry target values: TNT
RfactorNum. reflection% reflection
Rwork0.196 --
all-53039 -
obs-18916 92 %
Solvent computationBsol: 150 Å2 / ksol: 0.82 e/Å3
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1810 0 0 102 1912
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01336581
X-RAY DIFFRACTIONt_angle_deg1.7249343.1
X-RAY DIFFRACTIONt_dihedral_angle_d20.3621260
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.09981.5
X-RAY DIFFRACTIONt_gen_planes0.0135308
X-RAY DIFFRACTIONt_it4.436361.5
X-RAY DIFFRACTIONt_nbd0.045710
Software
*PLUS
Name: TNT / Version: 5F / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg20.360
X-RAY DIFFRACTIONt_planar_d0.091.5
X-RAY DIFFRACTIONt_plane_restr0.0138

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