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- PDB-5tjf: The crystal structure of Allophycocyanin from the red algae Graci... -

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Basic information

Entry
Database: PDB / ID: 5tjf
TitleThe crystal structure of Allophycocyanin from the red algae Gracilaria chilensis
Components(Allophycocyanin ...) x 2
KeywordsPHOTOSYNTHESIS / allophycocianin / phycobilisome / phycobiliproteins / FRET
Function / homology
Function and homology information


phycobilisome / chloroplast thylakoid membrane / photosynthesis
Similarity search - Function
Allophycocyanin, 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 / DI(HYDROXYETHYL)ETHER / Allophycocyanin alpha subunit / Allophycocyanin beta subunit
Similarity search - Component
Biological speciesGracilaria chilensis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsFigueroa, M. / Dagnino, J. / Kerff, F. / Chartier, P. / Bunster, M. / Martinez-Oyanedel, J.
Funding support Chile, 1items
OrganizationGrant numberCountry
CONICYTFONDECYT 113.0256 Chile
CitationJournal: PLoS ONE / Year: 2017
Title: Structural models of the different trimers present in the core of phycobilisomes from Gracilaria chilensis based on crystal structures and sequences.
Authors: Dagnino-Leone, J. / Figueroa, M. / Mella, C. / Vorphal, M.A. / Kerff, F. / Vasquez, A.J. / Bunster, M. / Martinez-Oyanedel, J.
History
DepositionOct 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references / Derived calculations / Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Allophycocyanin alpha subunit
B: Allophycocyanin beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,07630
Polymers34,9062
Non-polymers2,17028
Water8,611478
1
A: Allophycocyanin alpha subunit
B: Allophycocyanin beta subunit
hetero molecules

A: Allophycocyanin alpha subunit
B: Allophycocyanin beta subunit
hetero molecules

A: Allophycocyanin alpha subunit
B: Allophycocyanin beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,22790
Polymers104,7176
Non-polymers6,51084
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_985-y+4,x-y+3,z1
crystal symmetry operation3_695-x+y+1,-x+4,z1
Unit cell
Length a, b, c (Å)97.410, 97.410, 63.830
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-310-

HOH

21A-327-

HOH

31A-397-

HOH

41A-463-

HOH

51A-468-

HOH

61A-495-

HOH

71A-515-

HOH

81A-517-

HOH

91B-331-

HOH

101B-380-

HOH

111B-467-

HOH

121B-490-

HOH

131B-546-

HOH

141B-549-

HOH

151B-551-

HOH

161B-554-

HOH

171B-555-

HOH

181B-556-

HOH

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Components

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Allophycocyanin ... , 2 types, 2 molecules AB

#1: Protein Allophycocyanin alpha subunit


Mass: 17403.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gracilaria chilensis (eukaryote) / References: UniProt: A0A141SEH2
#2: Protein Allophycocyanin beta subunit


Mass: 17501.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gracilaria chilensis (eukaryote) / References: UniProt: A0A141SEH3

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Non-polymers , 5 types, 506 molecules

#3: Chemical ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C33H40N4O6
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 478 / 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: 2.43 Å3/Da / Density % sol: 49.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 18% PEG 6000 0.3 M NaCl 0.1 M MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.3→42.18 Å / Num. obs: 29513 / % possible obs: 97 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.1303 / Net I/σ(I): 8.43
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.3568 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 2.3→42.18 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.01 / Phase error: 32.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2839 1479 5.04 %
Rwork0.257 --
obs0.2584 29317 97.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→42.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2422 0 135 478 3035
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042567
X-RAY DIFFRACTIONf_angle_d1.5553468
X-RAY DIFFRACTIONf_dihedral_angle_d16.7531513
X-RAY DIFFRACTIONf_chiral_restr0.036386
X-RAY DIFFRACTIONf_plane_restr0.003445
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3002-2.37450.33221370.30182554X-RAY DIFFRACTION97
2.3745-2.45930.39511350.32552521X-RAY DIFFRACTION98
2.4593-2.55780.33661380.30542546X-RAY DIFFRACTION98
2.5578-2.67420.2971310.31012507X-RAY DIFFRACTION98
2.6742-2.81510.32171340.30542606X-RAY DIFFRACTION99
2.8151-2.99150.31441310.28942530X-RAY DIFFRACTION98
2.9915-3.22240.31391360.26662561X-RAY DIFFRACTION98
3.2224-3.54650.25441290.24982534X-RAY DIFFRACTION97
3.5465-4.05930.28881340.23162502X-RAY DIFFRACTION97
4.0593-5.11290.23741330.20922448X-RAY DIFFRACTION94
5.1129-42.18680.2261410.21792530X-RAY DIFFRACTION97

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