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- PDB-1f0b: CRYSTAL STRUCTURE OF THE GREEN FLUORESCENT PROTEIN (GFP) VARIANT ... -

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Basic information

Entry
Database: PDB / ID: 1f0b
TitleCRYSTAL STRUCTURE OF THE GREEN FLUORESCENT PROTEIN (GFP) VARIANT YFP-H148Q
ComponentsGREEN FLUORESCENT PROTEIN
KeywordsLUMINESCENT PROTEIN / beta barrel / luminescence / bioluminescence / photoactive protein / green fluorescent protein
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: 2.1 Å
AuthorsWachter, R.M. / Yarbrough, D. / Kallio, K. / Remington, S.J.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Crystallographic and energetic analysis of binding of selected anions to the yellow variants of green fluorescent protein.
Authors: Wachter, R.M. / Yarbrough, D. / Kallio, K. / Remington, S.J.
#1: Journal: CURR.BIOL. / Year: 1999
Title: Sensitivity of the Yellow Variant of Green Fluorescent Protein to Halides and Nitrate
Authors: Wachter, R.M. / Remington, S.J.
History
DepositionMay 15, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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 1.4Oct 30, 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: GREEN FLUORESCENT PROTEIN


Theoretical massNumber of molelcules
Total (without water)26,9511
Polymers26,9511
Non-polymers00
Water2,252125
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.661, 62.646, 66.183
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 GREEN FLUORESCENT PROTEIN / GFP


Mass: 26951.408 Da / Num. of mol.: 1 / Mutation: S65G, V68L, S72A, Q80R, T203Y, H148Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Plasmid: BL21DE3 / Production host: Escherichia coli (E. coli) / References: UniProt: P42212
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 1.98 Å3/Da / Density % sol: 38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 1550, sodium acetate, magnesium chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.9
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
220 mMTris1drop
322 %(w/v)PEG15501reservoir
4100 mMsodium acetate1reservoir
590 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 4, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.07→22.5 Å / Num. all: 29297 / Num. obs: 11419 / % possible obs: 82.1 % / Redundancy: 2.56 % / Biso Wilson estimate: 25.3 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 10.3
Reflection shellResolution: 2.07→2.15 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.32 / Num. unique all: 1106 / % possible all: 81.5
Reflection
*PLUS
Num. measured all: 29297
Reflection shell
*PLUS
% possible obs: 81.5 %

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Processing

Software
NameClassification
TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling
TNTphasing
RefinementResolution: 2.1→22.5 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rwork0.188 --
all0.188 11402 -
obs0.188 11402 81.5 %
Refinement stepCycle: LAST / Resolution: 2.1→22.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1816 0 0 125 1941
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.02
X-RAY DIFFRACTIONt_angle_deg3.06
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_angle_deg / Dev ideal: 3.06

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