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- PDB-5ez2: Sandercyanin Fluorescent Protein (SFP) -

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Basic information

Entry
Database: PDB / ID: 5ez2
TitleSandercyanin Fluorescent Protein (SFP)
ComponentsSandercyanin Fluorescent Protein
KeywordsFLUORESCENT PROTEIN / Sandercyanin / red-fluorescent protein / lipocalin / biliverdin / photo-stability
Function / homology
Function and homology information


pigment binding / response to reactive oxygen species / lipid metabolic process / cytoplasm
Similarity search - Function
Lipocalin-like domain / Invertebrate colouration protein / Lipocalin, ApoD type / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
BILIVERDINE IX ALPHA / Apolipoprotein D
Similarity search - Component
Biological speciesSander vitreus (walleye)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.849 Å
AuthorsGhosh, S. / Ramaswamy, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Blue protein with red fluorescence
Authors: Ghosh, S. / Yu, C.L. / Ferraro, D.J. / Sudha, S. / Pal, S.K. / Schaefer, W.F. / Gibson, D.T. / Ramaswamy, S.
History
DepositionNov 26, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sandercyanin Fluorescent Protein
B: Sandercyanin Fluorescent Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7959
Polymers40,3192
Non-polymers1,4767
Water5,639313
1
A: Sandercyanin Fluorescent Protein
B: Sandercyanin Fluorescent Protein
hetero molecules

A: Sandercyanin Fluorescent Protein
B: Sandercyanin Fluorescent Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,59018
Polymers80,6394
Non-polymers2,95114
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
Buried area14430 Å2
ΔGint-107 kcal/mol
Surface area27600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.266, 159.266, 84.157
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-546-

HOH

21B-564-

HOH

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Components

#1: Protein Sandercyanin Fluorescent Protein


Mass: 20159.748 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sander vitreus (walleye) / Tissue: Mucus / Cell line: Mucosa / Plasmid: pET21a
Details (production host): Ampicillin resistant plasmid, gene is cloned between NdeI and HindIII
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1D5B367*PLUS
#2: Chemical ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C33H34N4O6
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 4.12 Å3/Da / Density % sol: 70.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1M Bis-Tris, 1M NaCl, PEG 400 / Temp details: Crystals were grown in a cold incubator

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.987 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Oct 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.849→35.99 Å / Num. obs: 53181 / % possible obs: 98.47 % / Redundancy: 4 % / Net I/σ(I): 15.48
Reflection shellResolution: 1.849→1.915 Å

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
HKL-2000data processing
HKL-2000data scaling
PHASERphasing
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F6Z

5f6z


Resolution: 1.849→35.99 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2125 2000 3.76 %
Rwork0.1904 --
obs0.1912 53176 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.849→35.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2680 0 20 313 3013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072771
X-RAY DIFFRACTIONf_angle_d1.7353766
X-RAY DIFFRACTIONf_dihedral_angle_d13.527981
X-RAY DIFFRACTIONf_chiral_restr0.077398
X-RAY DIFFRACTIONf_plane_restr0.005484
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.849-1.89520.30291390.27723564X-RAY DIFFRACTION97
1.8952-1.94650.31241410.28173595X-RAY DIFFRACTION98
1.9465-2.00370.26161400.22243591X-RAY DIFFRACTION98
2.0037-2.06840.23391420.20493623X-RAY DIFFRACTION99
2.0684-2.14230.23051420.18963625X-RAY DIFFRACTION99
2.1423-2.22810.24731410.19793628X-RAY DIFFRACTION99
2.2281-2.32950.25451420.20343634X-RAY DIFFRACTION99
2.3295-2.45230.23321430.20543655X-RAY DIFFRACTION99
2.4523-2.60590.25531440.20353680X-RAY DIFFRACTION99
2.6059-2.8070.22751430.19693683X-RAY DIFFRACTION99
2.807-3.08930.21881460.18723707X-RAY DIFFRACTION100
3.0893-3.5360.21541450.17963725X-RAY DIFFRACTION99
3.536-4.45370.15831460.15993731X-RAY DIFFRACTION98
4.4537-35.99830.17691460.18383735X-RAY DIFFRACTION94

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