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- PDB-7vns: Sandercyanin mutant E79A-Biliverdin complex -

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Basic information

Entry
Database: PDB / ID: 7vns
TitleSandercyanin mutant E79A-Biliverdin complex
ComponentsSandercyanin Fluorescent Protein
KeywordsFLUORESCENT PROTEIN / Lipocalin / biliverdin
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 / Sandercyanin Fluorescent Protein
Similarity search - Component
Biological speciesSander vitreus (walleye)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsYadav, K. / Ghosh, S. / Subramanian, R.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR5801/INF/22/156/2012 India
CitationJournal: Febs Lett. / Year: 2022
Title: Phenylalanine stacking enhances the red fluorescence of biliverdin IX alpha on UV excitation in sandercyanin fluorescent protein.
Authors: Yadav, K. / Ghosh, S. / Barak, A. / Schaefer, W. / Subramanian, R.
History
DepositionOct 12, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)41,3694
Polymers40,2032
Non-polymers1,1652
Water6,882382
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)82,7378
Polymers80,4074
Non-polymers2,3314
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Buried area11360 Å2
ΔGint-123 kcal/mol
Surface area28670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.024, 160.024, 82.485
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Space group name HallP6c2c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z+1/2
#9: y,x,-z
#10: -y,-x,-z+1/2
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/2

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Components

#1: Protein Sandercyanin Fluorescent Protein


Mass: 20101.713 Da / Num. of mol.: 2 / Mutation: E79A
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.: 2 / Source method: isolated from a natural source / Formula: C33H34N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.81 Å3/Da / Density % sol: 67.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.4 M sodium potassium tartrate, 0.2M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9897 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9897 Å / Relative weight: 1
ReflectionResolution: 1.95→53.06 Å / Num. obs: 45772 / % possible obs: 100 % / Redundancy: 38.5 % / Biso Wilson estimate: 23.8 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.3
Reflection shellResolution: 1.95→2 Å / Num. unique obs: 3164 / CC1/2: 0.767 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
DIALSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EZ2

5ez2


Resolution: 1.95→52.38 Å / SU ML: 0.1493 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.1305
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1772 2288 5.01 %
Rwork0.1741 43404 -
obs0.1743 45692 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.77 Å2
Refinement stepCycle: LAST / Resolution: 1.95→52.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2592 0 86 382 3060
Refine LS restraintsType: f_plane_restr / Dev ideal: 0.0123 / Number: 484
LS refinement shellResolution: 1.95→1.99 Å
RfactorNum. reflection% reflection
Rfree0.2623 153 -
Rwork0.2337 2636 -
obs--99.5 %

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