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- PDB-6hrn: C-Phycocyanin from heterocyst forming filamentous cyanobacterium ... -

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Basic information

Entry
Database: PDB / ID: 6hrn
TitleC-Phycocyanin from heterocyst forming filamentous cyanobacterium Nostoc sp. WR13
Components
  • Alpha Subunit of Cyanobacterial Phycocyanin protein
  • Beta Subunit of Cyanobacterial Phycocyanin protein
KeywordsPHOTOSYNTHESIS / Heterocyst forming filamentous cyanobacterium / Phycobilisomes / Phycocyanin / CYC chromophores
Function / homology
Function and homology information


: / phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis
Similarity search - Function
Phycocyanin, alpha subunit / Phycocyanin, beta subunit / Phycocyanins / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globin-like / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHYCOCYANOBILIN / NITRATE ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION / Alpha Subunit of Cyanobacterial Phycocyanin protein / Beta Subunit of Cyanobacterial Phycocyanin protein
Similarity search - Component
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.513 Å
AuthorsPatel, H.M. / Roszak, A.W. / Madamwar, D. / Cogdell, R.J.
CitationJournal: Int.J.Biol.Macromol. / Year: 2019
Title: Crystal structure of phycocyanin from heterocyst-forming filamentous cyanobacterium Nostoc sp. WR13.
Authors: Patel, H.M. / Roszak, A.W. / Madamwar, D. / Cogdell, R.J.
History
DepositionSep 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha Subunit of Cyanobacterial Phycocyanin protein
B: Beta Subunit of Cyanobacterial Phycocyanin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,88217
Polymers35,3572
Non-polymers3,52515
Water6,648369
1
A: Alpha Subunit of Cyanobacterial Phycocyanin protein
B: Beta Subunit of Cyanobacterial Phycocyanin protein
hetero molecules

A: Alpha Subunit of Cyanobacterial Phycocyanin protein
B: Beta Subunit of Cyanobacterial Phycocyanin protein
hetero molecules

A: Alpha Subunit of Cyanobacterial Phycocyanin protein
B: Beta Subunit of Cyanobacterial Phycocyanin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,64551
Polymers106,0716
Non-polymers10,57545
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area36440 Å2
ΔGint-221 kcal/mol
Surface area38460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.473, 151.473, 39.764
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Alpha Subunit of Cyanobacterial Phycocyanin protein


Mass: 17323.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: There is one chromophore molecule, phycocyanobilin (ligand ID: CYC), bound covalently to C-Phycocyanin alpha subunit residue CYS84
Source: (natural) Nostoc sp. (bacteria) / Strain: WR13 / References: UniProt: A0A509GUZ8*PLUS
#2: Protein Beta Subunit of Cyanobacterial Phycocyanin protein


Mass: 18033.443 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: There are two chromophore molecules, phycocyanobilins (ligand ID: CYC), bound covalently to C-Phycocyanin beta subunit residues CYS82 and CYS153, respectively.
Source: (natural) Nostoc sp. (bacteria) / Strain: WR13 / References: UniProt: A0A509GUZ9*PLUS

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Non-polymers , 8 types, 384 molecules

#3: Chemical ChemComp-CYC / PHYCOCYANOBILIN / Phycocyanobilin


Mass: 588.694 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C33H40N4O6
#4: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#9: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H14O2 / Comment: precipitant*YM
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H2O

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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: 3.72 Å3/Da / Density % sol: 66.98 % / Description: hexagonal rod
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus crystallisation screen condition C4: 37.5% MPD_Peg1K_Peg3350 precipitant, 0.1M buffer system (imidazole & MES) and the NPS (nitrate, phosphate & sulfate) mix of additives.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.513→131.179 Å / Num. obs: 73328 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 27.18 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.016 / Rrim(I) all: 0.037 / Net I/σ(I): 20.5
Reflection shellResolution: 1.513→1.589 Å / Redundancy: 5.6 % / Rmerge(I) obs: 1.013 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3665 / CC1/2: 0.609 / Rpim(I) all: 0.47 / Rrim(I) all: 1.135 / % possible all: 54

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
XDS20180808data reduction
pointless1.11.14data scaling
Aimless0.7.2data scaling
autoPROC1.0.5data scaling
STARANISO1.10.15data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: not published yet

Resolution: 1.513→75.75 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.979 / SU B: 2.602 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.052 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15396 3582 4.9 %RANDOM
Rwork0.11487 ---
obs0.11678 69746 89.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.086 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20.24 Å20 Å2
2--0.48 Å20 Å2
3----1.57 Å2
Refinement stepCycle: 1 / Resolution: 1.513→75.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2478 0 245 369 3092
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132850
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172679
X-RAY DIFFRACTIONr_angle_refined_deg1.6121.6553853
X-RAY DIFFRACTIONr_angle_other_deg1.4911.586195
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1525358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.1720.604149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.16115420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2021519
X-RAY DIFFRACTIONr_chiral_restr0.0930.2367
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023260
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02572
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_it4.4134.1991363
X-RAY DIFFRACTIONr_mcbond_other4.3894.1971362
X-RAY DIFFRACTIONr_mcangle_it5.3966.3031708
X-RAY DIFFRACTIONr_mcangle_other5.3956.3051709
X-RAY DIFFRACTIONr_scbond_it6.4284.7221487
X-RAY DIFFRACTIONr_scbond_other6.4264.7211488
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.0996.8782134
X-RAY DIFFRACTIONr_long_range_B_refined7.5453.6043350
X-RAY DIFFRACTIONr_long_range_B_other7.07752.6893259
X-RAY DIFFRACTIONr_rigid_bond_restr3.65735529
X-RAY DIFFRACTIONr_sphericity_free40.6275226
X-RAY DIFFRACTIONr_sphericity_bonded28.855620
LS refinement shellResolution: 1.513→1.553 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 48 -
Rwork0.269 1083 -
obs--18.82 %

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