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- PDB-1g7k: CRYSTAL STRUCTURE OF DSRED, A RED FLUORESCENT PROTEIN FROM DISCOS... -

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Basic information

Entry
Database: PDB / ID: 1g7k
TitleCRYSTAL STRUCTURE OF DSRED, A RED FLUORESCENT PROTEIN FROM DISCOSOMA SP. RED
ComponentsFLUORESCENT PROTEIN FP583
KeywordsLUMINESCENT PROTEIN / Fluorescent Protein / GFP / Coral / Red / Beta Barrel / Chromophore / dsred / drFP583
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
Red fluorescent protein drFP583
Similarity search - Component
Biological speciesDiscosoma sp. (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsYarbrough, D. / Wachter, R.M. / Kallio, K. / Matz, M.V. / Remington, S.J.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Refined crystal structure of DsRed, a red fluorescent protein from coral, at 2.0-A resolution.
Authors: Yarbrough, D. / Wachter, R.M. / Kallio, K. / Matz, M.V. / Remington, S.J.
#1: Journal: Nat.Biotechnol. / Year: 1999
Title: Fluorescent Proteins from Nonbioluminescent Anthozoa Species
Authors: Matz, M.V. / Fradkov, A.F. / Labas, Y.A. / Savitsky, A.P. / Zaraisky, A.G. / Markelov, M.L. / Lukyanov, S.A.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: The Structure of the Chromophore within DsRed, a Red Fluorescent Protein from Coral
Authors: Gross, L.A. / Baird, G.S. / Hoffman, R.C. / Baldridge, K.K. / Tsien, R.Y.
History
DepositionNov 10, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_torsion / struct_conn / struct_ref_seq_dif
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details
Revision 2.1Oct 30, 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:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FLUORESCENT PROTEIN FP583
B: FLUORESCENT PROTEIN FP583
C: FLUORESCENT PROTEIN FP583
D: FLUORESCENT PROTEIN FP583


Theoretical massNumber of molelcules
Total (without water)110,2054
Polymers110,2054
Non-polymers00
Water7,530418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9230 Å2
ΔGint-28 kcal/mol
Surface area31000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.366, 112.270, 70.691
Angle α, β, γ (deg.)90.00, 93.81, 90.00
Int Tables number4
Space group name H-MP1211
Detailsthe full biological assembly is the homotetramer in the asymmetric unit

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Components

#1: Protein
FLUORESCENT PROTEIN FP583 / DSRED


Mass: 27551.205 Da / Num. of mol.: 4 / Mutation: RESIDUES 66-68 REPLACED BY CRO
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Discosoma sp. (sea anemone) / Gene: DRFP583 / Plasmid: PQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): JM-109 / References: UniProt: Q9U6Y8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRESIDUES GLN 66, TYR 67, GLY 68 ARE MODIFIED TO MAKE THE CHROMOPHORE CRQ 66.

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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: 2.02 Å3/Da / Density % sol: 39.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: PEG 4000, Tris, Beta-Mercaptoethanol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.9 / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12 mMbeta-mercaptoethanol1drop
2300 mM1dropNaCl
320 mMTris1drop
415 mg/mlprotein1drop
516 %PEG15501reservoir
60.1 MTris1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97887,0.97868,0.95373
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 21, 1999 / Details: mirrors
RadiationMonochromator: Double-Crystal Si 111 crystals / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978871
20.978681
30.953731
ReflectionResolution: 2→24.1 Å / Num. all: 56056 / Num. obs: 56056 / % possible obs: 94.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 10.2 Å2 / Rmerge(I) obs: 0.026 / Net I/σ(I): 18.6
Reflection shellResolution: 2→2.1 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.043 / % possible all: 95.1
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 25.1 Å / Num. obs: 56118 / Num. measured all: 232348 / Rmerge(I) obs: 0.027
Reflection shell
*PLUS
Lowest resolution: 2.11 Å / Rmerge(I) obs: 0.044

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Processing

Software
NameClassification
SHARPphasing
TNTrefinement
MOSFLMdata reduction
FHSCALEdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: TNT
RfactorNum. reflection% reflectionSelection details
Rfree0.249 5654 -random
Rwork0.162 ---
all0.166 60778 --
obs0.166 56328 93 %-
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7168 0 0 418 7586
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg1.859
X-RAY DIFFRACTIONt_bond_d0.014
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 25.1 Å / σ(F): 0 / Rfactor obs: 0.162
Solvent computation
*PLUS
Displacement parameters
*PLUS

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