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- PDB-3o2c: Crystal structure of a rod form of c-phycocyanin from Themosynech... -

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Basic information

Entry
Database: PDB / ID: 3o2c
TitleCrystal structure of a rod form of c-phycocyanin from Themosynechococcus vulcanus at 1.5 angstroms
Components
  • C-phycocyanin alpha subunit
  • C-phycocyanin beta subunit
KeywordsPHOTOSYNTHESIS / Phycobilisome / Cyanobacteria / Light Harvesting
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 / C-phycocyanin beta subunit / C-phycocyanin alpha subunit
Similarity search - Component
Biological speciesThermosynechococcus vulcanus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsDavid, L. / Marx, A. / Adir, N.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: High-resolution crystal structures of trimeric and rod phycocyanin.
Authors: David, L. / Marx, A. / Adir, N.
History
DepositionJul 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,4535
Polymers35,6872
Non-polymers1,7663
Water8,269459
1
A: C-phycocyanin alpha subunit
B: C-phycocyanin beta subunit
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)112,36015
Polymers107,0626
Non-polymers5,2989
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area24300 Å2
ΔGint-234 kcal/mol
Surface area39860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.469, 187.469, 60.180
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
DetailsAuthors state that phycocyanin forms hexamers which elongate into rod structures, a subcomponent of a large complex called the phycobilisome.

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Components

#1: Protein C-phycocyanin alpha subunit


Mass: 17470.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: Q9AM02
#2: Protein C-phycocyanin beta subunit


Mass: 18216.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: Q71RW8
#3: Chemical ChemComp-CYC / PHYCOCYANOBILIN / Phycocyanobilin


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


Mass: 18.015 Da / Num. of mol.: 459 / 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: 2.85 Å3/Da / Density % sol: 56.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.2M phosphate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9795 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→93.735 Å / Num. all: 63473 / Num. obs: 63473 / % possible obs: 98.8 % / Redundancy: 3.8 % / Rsym value: 0.019 / Net I/σ(I): 71.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.5-1.583.80.2042.93421289310.20495.7
1.58-1.683.80.1583.73283486160.15897.7
1.68-1.793.80.11453112082490.11499.2
1.79-1.943.80.0757.72904477230.07599.7
1.94-2.123.60.03614.42556171010.03699.7
2.12-2.373.60.02126.12348164480.02199.8
2.37-2.743.80.01437.52161357150.01499.9
2.74-3.353.90.00958.31904748470.00999.9
3.35-4.743.80.00763.61442037550.007100
4.74-25.9973.90.00747.5822820880.00798.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 35.9 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å26 Å
Translation2.5 Å26 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
PHASER2.1.4phasing
CNS1.1refinement
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→26 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.934 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 0.001 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2631 3193 5.1 %RANDOM
Rwork0.239 ---
obs0.2403 63024 98.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 73.4 Å2 / Biso mean: 20.6126 Å2 / Biso min: 7.92 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.38 Å
Refinement stepCycle: LAST / Resolution: 1.5→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2500 0 129 459 3088
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.020524
X-RAY DIFFRACTIONc_angle_d1.65891
X-RAY DIFFRACTIONc_dihedral_angle_d19.07078
X-RAY DIFFRACTIONc_improper_angle_d2.56403
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 205 -
Rwork0.428 4225 -
all-4430 -
obs--93.9 %

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