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- PDB-7d6w: Crystal structure of Phycocyanin from Synechococcus sp. R42DM -

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Basic information

Entry
Database: PDB / ID: 7d6w
TitleCrystal structure of Phycocyanin from Synechococcus sp. R42DM
Components
  • Phycocyanin alpha subunit
  • Phycocyanin beta subunit
KeywordsPHOTOSYNTHESIS / light harvesting property
Function / homologyPHYCOCYANOBILIN
Function and homology information
Biological speciesSynechococcus sp. R42DM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsPatel, S.N. / Sonani, R.R. / Chaubey, M.G. / Singh, N.K. / Kumar, V. / Madamwar, D.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR15686/AAQ/3/811/2016 India
CitationJournal: 3 Biotech / Year: 2023
Title: Crystal structure of Synechococcus phycocyanin: implications of light-harvesting and antioxidant properties.
Authors: Patel, S.N. / Sonani, R.R. / Chaubey, M.G. / Gupta, G.D. / Singh, N.K. / Kumar, V. / Madamwar, D.
History
DepositionOct 2, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2023Group: Database references / Derived calculations / Category: atom_type / citation / citation_author
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 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: Phycocyanin alpha subunit
B: Phycocyanin beta subunit
C: Phycocyanin alpha subunit
D: Phycocyanin beta subunit
E: Phycocyanin alpha subunit
F: Phycocyanin beta subunit
G: Phycocyanin alpha subunit
H: Phycocyanin beta subunit
I: Phycocyanin alpha subunit
J: Phycocyanin beta subunit
K: Phycocyanin alpha subunit
L: Phycocyanin beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,65230
Polymers212,05612
Non-polymers10,59618
Water30,5351695
1
A: Phycocyanin alpha subunit
B: Phycocyanin beta subunit
G: Phycocyanin alpha subunit
H: Phycocyanin beta subunit
K: Phycocyanin alpha subunit
L: Phycocyanin beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,32615
Polymers106,0286
Non-polymers5,2989
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24200 Å2
ΔGint-255 kcal/mol
Surface area39960 Å2
MethodPISA
2
C: Phycocyanin alpha subunit
D: Phycocyanin beta subunit
E: Phycocyanin alpha subunit
F: Phycocyanin beta subunit
I: Phycocyanin alpha subunit
J: Phycocyanin beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,32615
Polymers106,0286
Non-polymers5,2989
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24070 Å2
ΔGint-251 kcal/mol
Surface area39820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.630, 113.990, 183.590
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Phycocyanin alpha subunit


Mass: 17172.041 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. R42DM (bacteria)
#2: Protein
Phycocyanin beta subunit


Mass: 18170.545 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. R42DM (bacteria)
#3: Chemical
ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C33H40N4O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1695 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.63 Å3/Da / Density % sol: 53.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES pH 6.5, 10% (W/V) PEG 6000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.9795 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.15→96.842 Å / Num. obs: 122052 / % possible obs: 100 % / Redundancy: 6.4 % / CC1/2: 0.994 / Rmerge(I) obs: 0.124 / Net I/σ(I): 9.6
Reflection shellResolution: 2.15→2.19 Å / Rmerge(I) obs: 0.384 / Num. unique obs: 5976 / CC1/2: 0.894

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4H0M

4h0m


Resolution: 2.15→96.842 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2097 6335 -RANDOM
Rwork0.1649 ---
obs-121960 99.978 %-
Displacement parametersBiso max: 67.41 Å2 / Biso mean: 16.7186 Å2 / Biso min: 6.81 Å2
Refinement stepCycle: LAST / Resolution: 2.15→96.842 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14916 0 774 1695 17385
LS refinement shellResolution: 2.15→2.206 Å
RfactorNum. reflection
Rfree0.26 474
Rwork0.186 -
obs0.19 -
all-8910

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