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- PDB-5f1e: Apo protein of Sandercyanin -

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Basic information

Entry
Database: PDB / ID: 5f1e
TitleApo protein of Sandercyanin
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
Biological speciesSander vitreus (walleye)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 30, 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 1.3Oct 9, 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


Theoretical massNumber of molelcules
Total (without water)40,3192
Polymers40,3192
Non-polymers00
Water1,71195
1
A: Sandercyanin Fluorescent Protein
B: Sandercyanin Fluorescent Protein

A: Sandercyanin Fluorescent Protein
B: Sandercyanin Fluorescent Protein


Theoretical massNumber of molelcules
Total (without water)80,6394
Polymers80,6394
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/21
Buried area5910 Å2
ΔGint-45 kcal/mol
Surface area30640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.764, 158.764, 84.795
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'A' and (resseq 22:188 )
211chain 'B' and (resseq 22:188 )

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 70.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1M HEPES, 10% PEG 8000, 8% v/v Ethylene glycol / PH range: 7.4-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.7→53.4 Å / Num. obs: 17824 / % possible obs: 99.98 % / Redundancy: 36.7 % / Rsym value: 0.129 / Net I/σ(I): 31.48

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
iMOSFLMdata reduction
d*TREKdata scaling
d*TREKphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F6Z

5f6z


Resolution: 2.7→53.4 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2481 908 5.1 %0.246
Rwork0.1965 ---
obs0.199 17808 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→53.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2567 0 0 95 2662
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092636
X-RAY DIFFRACTIONf_angle_d1.0883586
X-RAY DIFFRACTIONf_dihedral_angle_d13.867943
X-RAY DIFFRACTIONf_chiral_restr0.071395
X-RAY DIFFRACTIONf_plane_restr0.005468
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1278X-RAY DIFFRACTIONPOSITIONAL
12B1278X-RAY DIFFRACTIONPOSITIONAL0.044
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.86920.26731500.23062741X-RAY DIFFRACTION100
2.8692-3.09070.2961420.22412761X-RAY DIFFRACTION100
3.0907-3.40170.2891630.21752771X-RAY DIFFRACTION100
3.4017-3.89380.2691650.19132780X-RAY DIFFRACTION100
3.8938-4.90520.18741470.17252832X-RAY DIFFRACTION100
4.9052-53.41170.24221410.19333015X-RAY DIFFRACTION100

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