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- PDB-4f0t: X-Ray Crystal Structure of Phycocyanin from Synechocystis sp. PCC 6803 -

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Basic information

Entry
Database: PDB / ID: 4f0t
TitleX-Ray Crystal Structure of Phycocyanin from Synechocystis sp. PCC 6803
Components
  • C-phycocyanin alpha chain
  • C-phycocyanin beta chain
KeywordsPHOTOSYNTHESIS / Component of the phycobilisome / photosynthetic antenna complex
Function / homology
Function and homology information


phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis
Similarity search - Function
Phycocyanin, alpha subunit / Phycocyanins / Phycocyanin, beta subunit / 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 / C-phycocyanin beta subunit / C-phycocyanin alpha subunit
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsMarx, A. / Adir, N.
CitationJournal: Biochim.Biophys.Acta / Year: 2013
Title: Allophycocyanin and phycocyanin crystal structures reveal facets of phycobilisome assembly.
Authors: Marx, A. / Adir, N.
History
DepositionMay 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C-phycocyanin alpha chain
B: C-phycocyanin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5255
Polymers35,7592
Non-polymers1,7663
Water3,909217
1
A: C-phycocyanin alpha chain
B: C-phycocyanin beta chain
hetero molecules

A: C-phycocyanin alpha chain
B: C-phycocyanin beta chain
hetero molecules

A: C-phycocyanin alpha chain
B: C-phycocyanin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,57515
Polymers107,2776
Non-polymers5,2989
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area24550 Å2
ΔGint-251 kcal/mol
Surface area40040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.020, 153.020, 40.060
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein C-phycocyanin alpha chain


Mass: 17602.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Kazusa / References: UniProt: Q54715
#2: Protein C-phycocyanin beta chain


Mass: 18156.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Kazusa / References: UniProt: Q54714
#3: Chemical ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C33H40N4O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 3.79 Å3/Da / Density % sol: 67.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 6% PEG 4000; 400mM MgSO4; 20mM Tris pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.25→40 Å / Num. all: 25948 / Num. obs: 25948 / % possible obs: 100 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 25.7
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 7.7 / Num. unique all: 3757 / % possible all: 100

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Processing

Software
NameClassification
PHASERphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→40 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.915 / SU B: 0.003 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24992 1316 5.1 %RANDOM
Rwork0.21614 ---
obs0.21784 24593 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20.18 Å20 Å2
2--0.36 Å20 Å2
3----0.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.25→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2511 0 129 217 2857
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 85 -
Rwork0.309 1788 -
obs--99.73 %

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