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- PDB-6fzn: SMURFP-Y56R mutant in complex with biliverdin -

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Basic information

Entry
Database: PDB / ID: 6fzn
TitleSMURFP-Y56R mutant in complex with biliverdin
ComponentssmURFP
KeywordsFLUORESCENT PROTEIN / smurfp / biliverdin / optoacustic / phycobiliprotein
Function / homologyPhycocyanins / Globin-like / Orthogonal Bundle / Mainly Alpha / Chem-9UY
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsJanowski, R. / Fuenzalida-Wernera, J.P. / Mishra, K. / Vetschera, P. / Weidenfeld, I. / Richter, K. / Niessing, D. / Ntziachristos, V. / Stiel, A.C.
CitationJournal: J. Struct. Biol. / Year: 2018
Title: Crystal structure of a biliverdin-bound phycobiliprotein: Interdependence of oligomerization and chromophorylation.
Authors: Fuenzalida-Werner, J.P. / Janowski, R. / Mishra, K. / Weidenfeld, I. / Niessing, D. / Ntziachristos, V. / Stiel, A.C.
History
DepositionMar 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Feb 20, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: smURFP
B: smURFP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0493
Polymers31,4622
Non-polymers5871
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-14 kcal/mol
Surface area13040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.550, 57.960, 52.110
Angle α, β, γ (deg.)90.00, 105.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein smURFP


Mass: 15731.174 Da / Num. of mol.: 2 / Mutation: Y56R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-9UY / 3-[5-[[(3~{R},4~{R})-3-ethenyl-4-methyl-5-oxidanylidene-3,4-dihydropyrrol-2-yl]methyl]-2-[[5-[(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1~{H}-pyrrol-2-yl]methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid / Billeverdin IXa, bound form


Mass: 586.678 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H38N4O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 1.97 Å3/Da / Density % sol: 37.64 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2% v/v 1,4-dioxane, 0.1 M Tris pH 8.0, 15% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.000009 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000009 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 8452 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 79.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Net I/σ(I): 10.83
Reflection shellResolution: 2.5→2.57 Å / Redundancy: 7 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.99 / CC1/2: 0.811 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XSCALEdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.94 / SU B: 17.114 / SU ML: 0.346 / Cross valid method: THROUGHOUT / ESU R Free: 0.349 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26258 461 5.5 %RANDOM
Rwork0.21211 ---
obs0.21475 7991 98.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 70 Å2
Baniso -1Baniso -2Baniso -3
1-5.75 Å20 Å2-3.19 Å2
2---1.56 Å2-0 Å2
3----2.17 Å2
Refinement stepCycle: 1 / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2102 0 43 10 2155
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192189
X-RAY DIFFRACTIONr_bond_other_d0.0020.022071
X-RAY DIFFRACTIONr_angle_refined_deg1.5611.992954
X-RAY DIFFRACTIONr_angle_other_deg0.96434794
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4785260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.54723.29997
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.29815394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5221518
X-RAY DIFFRACTIONr_chiral_restr0.0620.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212383
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02443
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8647.9941053
X-RAY DIFFRACTIONr_mcbond_other2.847.991052
X-RAY DIFFRACTIONr_mcangle_it4.62211.9661309
X-RAY DIFFRACTIONr_mcangle_other4.62311.9721310
X-RAY DIFFRACTIONr_scbond_it2.8418.4141136
X-RAY DIFFRACTIONr_scbond_other2.8398.4141137
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.76112.5031645
X-RAY DIFFRACTIONr_long_range_B_refined7.45594.8192534
X-RAY DIFFRACTIONr_long_range_B_other7.45794.8092535
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 34 -
Rwork0.345 558 -
obs--97.37 %

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