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- PDB-1f99: CRYSTAL STRUCTURE OF R-PHYCOCYANIN FROM POLYSIPHONIA AT 2.4 A RES... -

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Basic information

Entry
Database: PDB / ID: 1f99
TitleCRYSTAL STRUCTURE OF R-PHYCOCYANIN FROM POLYSIPHONIA AT 2.4 A RESOLUTION
Components(R-PHYCOCYANIN) x 2
KeywordsPHOTOSYNTHESIS / LIGHT HARVESTING PROTEIN / R-PHYCOCYANIN / electron trasnport
Function / homology
Function and homology information


: / : / phycobilisome / chloroplast 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
BILIVERDINE IX ALPHA / PHYCOCYANOBILIN / PHYCOERYTHROBILIN / R-phycocyanin alpha chain / R-phycocyanin beta chain
Similarity search - Component
Biological speciesPolysiphonia urceolata (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsLiang, D.C. / Jiang, T. / Chang, W.R.
CitationJournal: Biophys.J. / Year: 2001
Title: Crystal structure of R-phycocyanin and possible energy transfer pathways in the phycobilisome.
Authors: Jiang, T. / Zhang, J.P. / Chang, W.R. / Liang, D.C.
History
DepositionJul 9, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: R-PHYCOCYANIN
B: R-PHYCOCYANIN
K: R-PHYCOCYANIN
L: R-PHYCOCYANIN
M: R-PHYCOCYANIN
N: R-PHYCOCYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,09315
Polymers106,8016
Non-polymers5,2929
Water6,125340
1
A: R-PHYCOCYANIN
B: R-PHYCOCYANIN
K: R-PHYCOCYANIN
L: R-PHYCOCYANIN
M: R-PHYCOCYANIN
N: R-PHYCOCYANIN
hetero molecules

A: R-PHYCOCYANIN
B: R-PHYCOCYANIN
K: R-PHYCOCYANIN
L: R-PHYCOCYANIN
M: R-PHYCOCYANIN
N: R-PHYCOCYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,18630
Polymers213,60112
Non-polymers10,58418
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area61820 Å2
ΔGint-512 kcal/mol
Surface area66560 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)135.100, 135.100, 210.00
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsBioloogical assembly is alpha 6 and beta 6, The asymmetry unit is alpha 3 and beta 3,

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Components

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Protein , 2 types, 6 molecules AKMBLN

#1: Protein R-PHYCOCYANIN


Mass: 17584.719 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: alpha chain / Source: (natural) Polysiphonia urceolata (eukaryote) / References: UniProt: P59858
#2: Protein R-PHYCOCYANIN


Mass: 18015.488 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: beta chain / Source: (natural) Polysiphonia urceolata (eukaryote) / References: UniProt: P59859

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Non-polymers , 4 types, 349 molecules

#3: Chemical ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H34N4O6
#4: Chemical
ChemComp-CYC / PHYCOCYANOBILIN / Phycocyanobilin


Mass: 588.694 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C33H40N4O6
#5: Chemical ChemComp-PEB / PHYCOERYTHROBILIN / Phycoerythrobilin


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


Mass: 18.015 Da / Num. of mol.: 340 / 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: 4.48 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: The hanging-drop contains 6mg/ml R-phycocyanin, 0.05M Na2HPO4/NaH2PO4 and (NH4)2SO4 (pH7.0). The diffusion buffer contained 10%-20% (NH4)2SO4 and 10% NaCl, 0.05M Na2HPO4/NaH2PO4, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlprotein1drop
20.05 Msodium phosphate1drop
30.05 Mammonium phosphate1drop
410-20 %ammonium sulfate1reservoir
510 %1reservoirNaCl
60.05 Msodium phosphate1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Dec 10, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 266953 / Num. obs: 73674 / % possible obs: 75.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.12
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.375 / % possible all: 91.1
Reflection
*PLUS
Num. measured all: 266953
Reflection shell
*PLUS
% possible obs: 49 %

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Processing

Software
NameClassification
AMoREphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.4→8 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.239 5542 10 %random 10%
Rwork0.189 ---
all0.194 73675 --
obs0.189 54898 75.5 %-
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7482 0 387 340 8209
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg2.4

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