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- PDB-7o3k: Structure of a monomeric variant (L135E) of Sandercyanin fluoresc... -

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Basic information

Entry
Database: PDB / ID: 7o3k
TitleStructure of a monomeric variant (L135E) of Sandercyanin fluorescent protein bound to biliverdin IX-alpha
ComponentsSandercyanin Fluorescent Protein
KeywordsFLUORESCENT PROTEIN / Blue fish protein / lipocalin / Biliverdin-binding protein / red-fluorescent protein
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
Similarity search - Domain/homology
BILIVERDINE IX ALPHA / Apolipoprotein D
Similarity search - Component
Biological speciesSander vitreus (walleye)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsGhosh, S. / Yadav, K. / Ramaswamy, S.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)Grant BT/PR5801/INF/22/156/2012 India
CitationJournal: Rsc Adv / Year: 2022
Title: Modulation of biliverdin dynamics and spectral properties by Sandercyanin.
Authors: Ghosh, S. / Mondal, S. / Yadav, K. / Aggarwal, S. / Schaefer, W.F. / Narayana, C. / Subramanian, R.
History
DepositionApr 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sandercyanin Fluorescent Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7582
Polymers20,1761
Non-polymers5831
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-18 kcal/mol
Surface area8620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.810, 39.810, 119.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Sandercyanin Fluorescent Protein


Mass: 20175.705 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sander vitreus (walleye) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1D5B367
#2: Chemical ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H34N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.32 Å3/Da / Density % sol: 46.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 26mg/mL 10% (w/v) PEG 1000, 10% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.987 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Oct 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.75→39.81 Å / Num. obs: 4795 / % possible obs: 99.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 13.9 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.07 / Rrim(I) all: 0.13 / Net I/av σ(I): 9 / Net I/σ(I): 9
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 703 / CC1/2: 0.804 / Rpim(I) all: 0.35 / Rrim(I) all: 0.657 / % possible all: 98

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Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
PHENIX1.19_4092phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EZ2

5ez2


Resolution: 2.75→39.81 Å / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2505 240 5.01 %
Rwork0.2313 4548 -
obs0.2324 4788 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.99 Å2 / Biso mean: 40.5199 Å2 / Biso min: 27.19 Å2
Refinement stepCycle: final / Resolution: 2.75→39.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1271 0 43 14 1328
Biso mean--43.62 38.22 -
Num. residues----166
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2 / % reflection obs: 99 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.75-3.460.30381260.251222532379
3.47-39.810.22321140.222422952409

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