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- PDB-1ggx: RED FLUORESCENT PROTEIN (FP583 OR DSRED(CLONTECH)) FROM DISCOSOMA SP. -

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Basic information

Entry
Database: PDB / ID: 1ggx
TitleRED FLUORESCENT PROTEIN (FP583 OR DSRED(CLONTECH)) FROM DISCOSOMA SP.
ComponentsPROTEIN (FLUORESCENT PROTEIN FP583)
KeywordsLUMINESCENT PROTEIN / FLUORESCENT PROTEIN / CHROMOPHORE / GFP / RFP / FP583
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 / OTHER / Resolution: 1.9 Å
AuthorsWall, M.A. / Socolich, M.A. / Ranganathan, R.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: The structural basis for red fluorescence in the tetrameric GFP homolog DsRed.
Authors: Wall, M.A. / Socolich, M. / Ranganathan, R.
History
DepositionOct 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 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_rmsd_angle / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)103,7944
Polymers103,7944
Non-polymers00
Water10,431579
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9420 Å2
ΔGint-29 kcal/mol
Surface area31590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.206, 129.621, 57.441
Angle α, β, γ (deg.)90.00, 99.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PROTEIN (FLUORESCENT PROTEIN FP583) / RFP


Mass: 25948.600 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: RESIDUE CRQ 68 IS MADE FROM RESIDUES GLN 66, TYR 67 AND GLY 68.
Source: (gene. exp.) Discosoma sp. (sea anemone) / Plasmid: PRSETB / Cellular location (production host): CYTOPLASM / Gene (production host): DSRED / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 (DE3) / References: UniProt: Q9U6Y8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 579 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES GLN 66, TYR 67, GLY 68 ARE MODIFIED TO MAKE THE CHROMOPHORE CRQ 68. THE N OF CRQ 66 SHARES ...RESIDUES GLN 66, TYR 67, GLY 68 ARE MODIFIED TO MAKE THE CHROMOPHORE CRQ 68. THE N OF CRQ 66 SHARES A DOUBLE BOND WITH CA1 OF CRQ 68 WHICH IS SP2 HYBRIDIZED (PLANAR). THEREFORE, WHILE THE PEPTIDE BOND BETWEEN PHE 65 AND CRQ 68 MOST CLOSELY RESEMBLES A CIS PEPTIDE-BOND, THIS IS NOT A STANDARD PEPTIDE BOND. THERE ARE 6 RESONANCE FORMS OF CRQ.

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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: 1.99 Å3/Da / Density % sol: 38.17 %
Description: DATA FOR SEMET CRYSTALS WERE COLLECTED AT THE F" PEAK ONLY.
Crystal growpH: 8.5 / Details: pH 8.5
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
154 %MPD1reservoir
20.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→28.4 Å / Num. obs: 62456 / % possible obs: 97.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 13.5 Å2 / Rsym value: 0.086 / Net I/σ(I): 14.5
Reflection shellResolution: 1.9→2.02 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.401 / % possible all: 79
Reflection
*PLUS
Num. measured all: 525892 / Rmerge(I) obs: 0.086
Reflection shell
*PLUS
% possible obs: 79 % / Rmerge(I) obs: 0.401

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: OTHER / Resolution: 1.9→28.4 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.212 3800 6.1 %RANDOM
Rwork0.192 ---
obs0.192 62456 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.43 Å2 / ksol: 0.349 e/Å3
Displacement parametersBiso mean: 18.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.95 Å20 Å2-0.55 Å2
2--4.19 Å20 Å2
3----2.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.9→28.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7132 0 0 579 7711
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.21.5
X-RAY DIFFRACTIONc_mcangle_it1.72
X-RAY DIFFRACTIONc_scbond_it1.992
X-RAY DIFFRACTIONc_scangle_it2.882.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.305 200 2.3 %
Rwork0.256 8621 -
obs--79 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CRO_RFP_FQYG.PARAMCRO_RFP_FQYG.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.01

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