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- PDB-4h0m: X-Ray Crystal Structure of Phycocyanin from Synechococcus elongat... -

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Basic information

Entry
Database: PDB / ID: 4h0m
TitleX-Ray Crystal Structure of Phycocyanin from Synechococcus elongatus sp. PCC 7942
Components
  • C-phycocyanin alpha chain
  • C-phycocyanin beta chain
KeywordsPHOTOSYNTHESIS / Component of the phycobilisome / photosynthetic antenna complex
Function / homology
Function and homology information


: / : / phycobilisome / 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 speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
DepositionSep 9, 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
C: C-phycocyanin alpha chain
D: C-phycocyanin beta chain
E: C-phycocyanin alpha chain
F: C-phycocyanin beta chain
G: C-phycocyanin alpha chain
H: C-phycocyanin beta chain
I: C-phycocyanin alpha chain
J: C-phycocyanin beta chain
K: C-phycocyanin alpha chain
L: C-phycocyanin beta chain
M: C-phycocyanin alpha chain
N: C-phycocyanin beta chain
O: C-phycocyanin alpha chain
P: C-phycocyanin beta chain
Q: C-phycocyanin alpha chain
R: C-phycocyanin beta chain
S: C-phycocyanin alpha chain
T: C-phycocyanin beta chain
U: C-phycocyanin alpha chain
V: C-phycocyanin beta chain
W: C-phycocyanin alpha chain
X: C-phycocyanin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)448,45360
Polymers427,26024
Non-polymers21,19336
Water13,908772
1
A: C-phycocyanin alpha chain
B: C-phycocyanin beta chain
C: C-phycocyanin alpha chain
D: C-phycocyanin beta chain
E: C-phycocyanin alpha chain
F: C-phycocyanin beta chain
G: C-phycocyanin alpha chain
H: C-phycocyanin beta chain
I: C-phycocyanin alpha chain
J: C-phycocyanin beta chain
K: C-phycocyanin alpha chain
L: C-phycocyanin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,22630
Polymers213,63012
Non-polymers10,59618
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37640 Å2
ΔGint-225 kcal/mol
Surface area76510 Å2
MethodPISA
2
M: C-phycocyanin alpha chain
N: C-phycocyanin beta chain
O: C-phycocyanin alpha chain
P: C-phycocyanin beta chain
Q: C-phycocyanin alpha chain
R: C-phycocyanin beta chain
S: C-phycocyanin alpha chain
T: C-phycocyanin beta chain
U: C-phycocyanin alpha chain
V: C-phycocyanin beta chain
W: C-phycocyanin alpha chain
X: C-phycocyanin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,22630
Polymers213,63012
Non-polymers10,59618
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37700 Å2
ΔGint-232 kcal/mol
Surface area76480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.840, 113.520, 184.440
Angle α, β, γ (deg.)90.00, 89.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
C-phycocyanin alpha chain


Mass: 17303.238 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / Strain: PCC 7942 / References: UniProt: P13530
#2: Protein
C-phycocyanin beta chain


Mass: 18301.738 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / Strain: PCC 7942 / References: UniProt: P06539
#3: Chemical...
ChemComp-CYC / PHYCOCYANOBILIN / Phycocyanobilin


Mass: 588.694 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: C33H40N4O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 772 / 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: 2.62 Å3/Da / Density % sol: 53.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG 4000, 50mM tris pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.2→40 Å / Num. all: 195069 / Num. obs: 195069 / % possible obs: 87.7 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 7.5
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.259 / Mean I/σ(I) obs: 3 / Num. unique all: 29351 / % possible all: 90.5

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Processing

Software
NameVersionClassification
PHASERphasing
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→40 Å / Cor.coef. Fo:Fc: 0.884 / Cor.coef. Fo:Fc free: 0.816 / SU B: 0.001 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.236 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29487 9751 5 %RANDOM
Rwork0.242 ---
obs0.24464 185314 87.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.308 Å2
Baniso -1Baniso -2Baniso -3
1--1.29 Å20 Å2-0.51 Å2
2--1.84 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 2.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29832 0 1548 772 32152
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 760 -
Rwork0.272 14100 -
obs--90.52 %

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