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- PDB-7vnl: Sandercyanin mutant-F55A-Biliverdin complex -

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Basic information

Entry
Database: PDB / ID: 7vnl
TitleSandercyanin mutant-F55A-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: 1.93 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 11, 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)41,7216
Polymers40,1672
Non-polymers1,5544
Water3,765209
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)83,44212
Polymers80,3354
Non-polymers3,1078
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_455-x+y-1,y,-z+1/21
Buried area14350 Å2
ΔGint-127 kcal/mol
Surface area27390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.388, 158.388, 81.073
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: 20083.652 Da / Num. of mol.: 2 / Mutation: F55A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sander vitreus (walleye) / Production host: Escherichia coli BL21(DE3) (bacteria) / 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: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 3.67 Å3/Da / Density % sol: 66.5 % / Description: Rod shaped and hexagonal
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M sodium malonate pH 7, 12% PEG w/v 3350

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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: 1.93→79.12 Å / Num. obs: 45351 / % possible obs: 100 % / Redundancy: 74.4 % / Biso Wilson estimate: 35.59 Å2 / CC1/2: 1 / Rpim(I) all: 0.026 / Rrim(I) all: 0.229 / Net I/σ(I): 20.8
Reflection shellResolution: 1.93→2.03 Å / Redundancy: 74.8 % / Num. unique obs: 6479 / CC1/2: 0.586 / Rpim(I) all: 0.581 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
SCALA3.3.22data scaling
PHENIX1.15.2-3472phasing
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EZ2

5ez2


Resolution: 1.93→52.36 Å / SU ML: 0.2237 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.1849
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.225 2263 5.01 %
Rwork0.1933 42938 -
obs0.1949 45201 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.28 Å2
Refinement stepCycle: LAST / Resolution: 1.93→52.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2588 0 112 209 2909
Refine LS restraintsType: f_bond_d / Dev ideal: 0.0078 / Number: 2768
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.970.3241430.32462589X-RAY DIFFRACTION98.88
1.97-2.020.31531410.29692617X-RAY DIFFRACTION99.21
2.02-2.070.37171200.272656X-RAY DIFFRACTION99.36
2.07-2.120.26611470.22872627X-RAY DIFFRACTION99.57

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