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- PDB-1zgq: Crystal Structure of the Discosoma Red Fluorescent Protein (DsRed... -

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Basic information

Entry
Database: PDB / ID: 1zgq
TitleCrystal Structure of the Discosoma Red Fluorescent Protein (DsRed) Variant Q66M
ComponentsRed fluorescent protein drFP583
KeywordsLUMINESCENT PROTEIN / RFP / red / fluorescent protein / DsRed / drFP583 / chromophore / GFP / coral / beta barrel / beta can
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
DI(HYDROXYETHYL)ETHER / Red fluorescent protein drFP583
Similarity search - Component
Biological speciesDiscosoma sp. (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTubbs, J.L. / Tainer, J.A. / Getzoff, E.D.
CitationJournal: Biochemistry / Year: 2005
Title: Crystallographic structures of discosoma red fluorescent protein with immature and mature chromophores: linking Peptide bond trans-cis isomerization and acylimine formation in chromophore maturation.
Authors: Tubbs, J.L. / Tainer, J.A. / Getzoff, E.D.
History
DepositionApr 21, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 999SEQUENCE RESIDUES MET 66, TYR 67, GLY 68 ARE MODIFIED TO MAKE THE CHROMOPHORE NRQ 66.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Red fluorescent protein drFP583
B: Red fluorescent protein drFP583
C: Red fluorescent protein drFP583
D: Red fluorescent protein drFP583
E: Red fluorescent protein drFP583
F: Red fluorescent protein drFP583
G: Red fluorescent protein drFP583
H: Red fluorescent protein drFP583
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,46216
Polymers207,6138
Non-polymers8498
Water28,1751564
1
A: Red fluorescent protein drFP583
B: Red fluorescent protein drFP583
C: Red fluorescent protein drFP583
D: Red fluorescent protein drFP583
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,3379
Polymers103,8074
Non-polymers5315
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14460 Å2
ΔGint-33 kcal/mol
Surface area32040 Å2
MethodPISA
2
E: Red fluorescent protein drFP583
F: Red fluorescent protein drFP583
G: Red fluorescent protein drFP583
H: Red fluorescent protein drFP583
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,1257
Polymers103,8074
Non-polymers3183
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13670 Å2
ΔGint-41 kcal/mol
Surface area32360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.235, 87.981, 161.639
Angle α, β, γ (deg.)90.00, 96.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Red fluorescent protein drFP583 / DsRed


Mass: 25951.666 Da / Num. of mol.: 8 / Mutation: Q66M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Discosoma sp. (sea anemone) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q9U6Y8
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1564 / Source method: isolated from a natural source / Formula: H2O

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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: 2.52 Å3/Da / Density % sol: 50.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: PEG 8000, sodium chloride, phosphate-citrate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.999 / Wavelength: 0.999 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 162657 / Num. obs: 157512 / % possible obs: 97 % / Observed criterion σ(F): 0 / Rsym value: 0.064 / Net I/σ(I): 10
Reflection shellResolution: 1.9→1.97 Å / Mean I/σ(I) obs: 1.8 / Rsym value: 0.417 / % possible all: 88.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→37.78 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 230636.49 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.22 7494 5 %RANDOM
Rwork0.194 ---
all0.194 157512 --
obs0.194 148662 91.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 12.5442 Å2 / ksol: 0.312782 e/Å3
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 1.9→37.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14330 0 0 1620 15950
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.54
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.21.5
X-RAY DIFFRACTIONc_mcangle_it3.532
X-RAY DIFFRACTIONc_scbond_it4.532
X-RAY DIFFRACTIONc_scangle_it7.072.5
LS refinement shellHighest resolution: 1.9 Å / Total num. of bins used: 6 /
Num. reflection% reflection
Rwork19679 -
Rfree-5.1 %

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