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- PDB-1bfp: BLUE VARIANT OF GREEN FLUORESCENT PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1bfp
TitleBLUE VARIANT OF GREEN FLUORESCENT PROTEIN
ComponentsBLUE FLUORESCENT PROTEIN
KeywordsLUMINESCENCE / FLUORESCENT PROTEIN / BLUE EMISSION / MUTANT / FLUOROPHORE / BIOLUMINESCENSE
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: 2.1 Å
AuthorsWachter, R.M. / Remington, S.J.
Citation
Journal: Biochemistry / Year: 1997
Title: Crystal structure and photodynamic behavior of the blue emission variant Y66H/Y145F of green fluorescent protein.
Authors: Wachter, R.M. / King, B.A. / Heim, R. / Kallio, K. / Tsien, R.Y. / Boxer, S.G. / Remington, S.J.
#1: Journal: Curr.Biol. / Year: 1996
Title: Engineering Green Fluorescent Protein for Improved Brightness, Longer Wavelengths and Fluorescence Resonance Energy Transfer
Authors: Heim, R. / Tsien, R.Y.
History
DepositionApr 9, 1997Processing site: BNL
Revision 1.0Jul 7, 1997Provider: 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 2, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BLUE FLUORESCENT PROTEIN


Theoretical massNumber of molelcules
Total (without water)26,8911
Polymers26,8911
Non-polymers00
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.010, 63.090, 69.180
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 BLUE FLUORESCENT PROTEIN / BLUE-EMISSION VARIANT


Mass: 26891.338 Da / Num. of mol.: 1 / Mutation: S65, H66, AND G67 ARE REPLACED WITH IIC 66, Y145F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Description: THE N-TERMINAL HIS-TAG HAS BEEN REMOVED / 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.: 82 / 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: 2.11 Å3/Da / Density % sol: 41.7 % / Description: ISOMORPHOUS REPLACEMENT
Crystal growTemperature: 277 K / pH: 4.5
Details: PROTEIN WAS CRYSTALLIZED AT 4 DEGC FROM 100MM SODIUM ACETATE PH 4.5 AND 10-12% PEG3400., temperature 277K
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 mg/mlprotein1drop
210 mMHEPES1drop
3100 mMsodium acetate1reservoir
410-12 %PEG34001reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Sep 19, 1996 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 12044 / % possible obs: 87 % / Observed criterion σ(I): 0 / Redundancy: 2.64 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 12.7
Reflection shellResolution: 2.1→2.26 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 2.24 / % possible all: 64
Reflection
*PLUS
Num. measured all: 31786
Reflection shell
*PLUS
% possible obs: 65 %

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Processing

Software
NameClassification
TNTrefinement
DATACdata reduction
SCALE1data scaling
TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EMA

1ema


Resolution: 2.1→20 Å / Isotropic thermal model: TNT / σ(F): 0 / Stereochemistry target values: TNT
RfactorNum. reflection% reflection
Rwork0.181 --
obs-31786 87 %
Solvent computationBsol: 300 Å2 / ksol: 0.8 e/Å3
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1784 0 0 82 1866
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0118281.5
X-RAY DIFFRACTIONt_angle_deg1.9724653
X-RAY DIFFRACTIONt_dihedral_angle_d20.0910640
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.012472
X-RAY DIFFRACTIONt_gen_planes0.0172666
X-RAY DIFFRACTIONt_it5.17718031.5
X-RAY DIFFRACTIONt_nbd0.0332410
Software
*PLUS
Name: TNT / Version: 5F / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_planar_d0.0122
X-RAY DIFFRACTIONt_plane_restr0.0176

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