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- PDB-2h8q: Crystal Structure of a Redshifted Mutant (K83M) of the Red Fluore... -

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Basic information

Entry
Database: PDB / ID: 2h8q
TitleCrystal Structure of a Redshifted Mutant (K83M) of the Red Fluorescent Protein dRFP583/dsRed
ComponentsRed fluorescent protein drFP583
KeywordsLUMINESCENT PROTEIN / beta barrel / fluorescent / red shift / GFP / dsRED / bioluminescence
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 / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYarbrough, C.A. / Remington, S.J.
CitationJournal: Biochemistry / Year: 2006
Title: Novel Chromophores and Buried Charges Control Color in mFruits(,).
Authors: Shu, X. / Shaner, N.C. / Yarbrough, C.A. / Tsien, R.Y. / Remington, S.J.
History
DepositionJun 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 20, 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_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Remark 999SEQUENCE The residues Gln 66, Tyr 67 and Gly 68 constitute the chromophore CRQ

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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


Theoretical massNumber of molelcules
Total (without water)100,9794
Polymers100,9794
Non-polymers00
Water10,449580
1
A: Red fluorescent protein drFP583
B: Red fluorescent protein drFP583

A: Red fluorescent protein drFP583
B: Red fluorescent protein drFP583


Theoretical massNumber of molelcules
Total (without water)100,9794
Polymers100,9794
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_656-x+y+1,y,-z+3/21
Buried area9410 Å2
ΔGint-25 kcal/mol
Surface area29180 Å2
MethodPISA, PQS
2
C: Red fluorescent protein drFP583
D: Red fluorescent protein drFP583

C: Red fluorescent protein drFP583
D: Red fluorescent protein drFP583


Theoretical massNumber of molelcules
Total (without water)100,9794
Polymers100,9794
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+5/31
Buried area9470 Å2
ΔGint-27 kcal/mol
Surface area29120 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)92.934, 92.934, 431.593
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsThe biological assembly is a tetramer generated by the operations: -x+1, y, -z+3/2 for chain A and B; or -0.5x+0.866y, 0.866x+0.5y, -z+5/3 for chain C and D.

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Components

#1: Protein
Red fluorescent protein drFP583 / DsRed


Mass: 25244.789 Da / Num. of mol.: 4 / Mutation: K83M
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 / Water


Mass: 18.015 Da / Num. of mol.: 580 / 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: 2.66 Å3/Da / Density % sol: 53.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M HEPES, 45%MPD dissolved in 1:1 ratio by volume of ~15mg/ml protein, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 23, 2001
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 65283 / % possible obs: 86.2 % / Rmerge(I) obs: 0.082 / Χ2: 1.08 / Net I/σ(I): 7.1
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 20.7 / Num. unique all: 3742 / Rsym value: 0.082 / Χ2: 0.248 / % possible all: 50.5

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Phasing

Phasing MRRfactor: 0.825 / Cor.coef. Fo:Fc: 0.106
Highest resolutionLowest resolution
Translation4 Å15 Å

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Processing

Software
NameVersionClassificationNB
HKL-2000data scaling
EPMR2.5phasing
TNTrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G7K

1g7k


Resolution: 2→5 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.268 --RANDOM
Rwork0.23 ---
all0.23 61886 --
obs-56843 80 %-
Displacement parametersBiso mean: 46.926 Å2
Baniso -1Baniso -2Baniso -3
1-2.88 Å22.88 Å20 Å2
2--2.88 Å20 Å2
3----5.77 Å2
Refinement stepCycle: LAST / Resolution: 2→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7044 0 0 580 7624
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.019107000.8
X-RAY DIFFRACTIONt_angle_deg2.966140361.4
X-RAY DIFFRACTIONt_dihedral_angle_d18.79267280
X-RAY DIFFRACTIONt_trig_c_planes0.0141562
X-RAY DIFFRACTIONt_gen_planes0.01718965
X-RAY DIFFRACTIONt_nbd0.06419110
X-RAY DIFFRACTIONt_it5.61106721
LS refinement shell
Resolution (Å)Refine-ID
2-2.07X-RAY DIFFRACTION
2.07-2.15X-RAY DIFFRACTION
2.15-2.25X-RAY DIFFRACTION
2.25-2.37X-RAY DIFFRACTION
2.37-2.52X-RAY DIFFRACTION
2.52-2.71X-RAY DIFFRACTION

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