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- PDB-7yx1: Sandercyanin fluorescent protein - Y142A variant bound to BV -

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Basic information

Entry
Database: PDB / ID: 7yx1
TitleSandercyanin fluorescent protein - Y142A variant bound to BV
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 / lipid binding / extracellular region / 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 (fish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsSubramanian, R. / Ghosh, S. / Yadav, K.
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
DepositionFeb 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
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
B: Sandercyanin Fluorescent Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3014
Polymers40,1352
Non-polymers1,1652
Water2,198122
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)82,6018
Polymers80,2714
Non-polymers2,3314
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_455-x+y-1,y,-z+1/21
Buried area11810 Å2
ΔGint-128 kcal/mol
Surface area28580 Å2
Unit cell
Length a, b, c (Å)161.329, 161.329, 82.165
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11B-429-

HOH

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Components

#1: Protein Sandercyanin Fluorescent Protein


Mass: 20067.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sander (fish) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1D5B367
#2: Chemical ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H34N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 3.86 Å3/Da / Density % sol: 68.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1M Bis-Tris pH 5.5 and 3M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.65→46.57 Å / Num. obs: 18760 / % possible obs: 99.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 14.93 Å2 / CC1/2: 0.928 / Rmerge(I) obs: 0.35 / Rpim(I) all: 0.139 / Rrim(I) all: 0.378 / Net I/σ(I): 5.1 / Num. measured all: 125211 / Scaling rejects: 483
Reflection shell

Diffraction-ID: 1 / Resolution: 2.65→2.78 Å

Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
5.50.57624190.2170.2620.63598.9
7.50.1365970.9890.050.14598.6

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Processing

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

5ez2


Resolution: 2.65→46.57 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.44 / Phase error: 21.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2804 920 4.91 %
Rwork0.2233 17833 -
obs0.226 18753 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.71 Å2 / Biso mean: 20.342 Å2 / Biso min: 1.78 Å2
Refinement stepCycle: final / Resolution: 2.65→46.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2580 0 86 122 2788
Biso mean--22.79 15.74 -
Num. residues----338
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.65-2.790.32111330.28622459259299
2.79-2.960.3241220.282425022624100
2.96-3.190.33951540.273824822636100
3.19-3.510.30781240.226125362660100
3.51-4.020.2621160.204225612677100
4.02-5.060.22181270.159425832710100
5.06-46.570.2341440.19722710285499

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