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- PDB-1jbo: The 1.45A Three-Dimensional Structure of c-Phycocyanin from the T... -

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Basic information

Entry
Database: PDB / ID: 1jbo
TitleThe 1.45A Three-Dimensional Structure of c-Phycocyanin from the Thermophylic Cyanobacterium Synechococcus elongatus
Components
  • C-Phycocyanin alpha chain
  • C-Phycocyanin beta chain
KeywordsPHOTOSYNTHESIS
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 alpha subunit / C-phycocyanin beta subunit
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsNield, J. / Rizkallah, P.J. / Barber, J. / Chayen, N.E.
CitationJournal: J.STRUCT.BIOL. / Year: 2003
Title: The 1.45A three-dimensional structure of C-phycocyanin from the thermophilic cyanobacterium Synechococcus elongatus
Authors: Nield, J. / Rizkallah, P.J. / Barber, J. / Chayen, N.E.
History
DepositionMay 2, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)37,4395
Polymers35,6732
Non-polymers1,7663
Water8,539474
1
A: C-Phycocyanin alpha chain
B: C-Phycocyanin beta chain
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)224,63630
Polymers214,04012
Non-polymers10,59618
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area60270 Å2
ΔGint-507 kcal/mol
Surface area69500 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)187.995, 187.995, 60.542
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-734-

HOH

21B-504-

HOH

DetailsThe biological assembly is a hexamer generated from the contents of the asymmetric unit by applying the operations: -y,x-y+1,z ; -x+y-1,-x,z ; y-1,x+1,-z ; x-y,-y+1,-z ; -x-1,-x+y,-z

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Components

#1: Protein C-Phycocyanin alpha chain


Mass: 17456.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / References: UniProt: P50032
#2: Protein C-Phycocyanin beta chain


Mass: 18216.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / References: UniProt: P50033
#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.: 474 / 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: 2.88 Å3/Da / Density % sol: 57.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: Ammonium Sulphate, MES, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.1 Mammonium sulfate1reservoir
240 mMMES1reservoirpH6.1
320 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.244 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 4, 2000
RadiationMonochromator: Sagitally focused Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.244 Å / Relative weight: 1
ReflectionResolution: 1.45→56.7 Å / Num. obs: 71757 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 16.34 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 5.7
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 2.5 / Num. unique all: 10410 / % possible all: 99.7
Reflection
*PLUS
Lowest resolution: 95 Å / Num. measured all: 485268
Reflection shell
*PLUS
% possible obs: 99.7 % / Num. unique obs: 10410 / Num. measured obs: 39957

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1CPC

1cpc


Resolution: 1.45→56.7 Å / Isotropic thermal model: Mixed isotropic and anisotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: REFMAC5 4.1 / Details: Weighted diagonal matrix
RfactorNum. reflectionSelection details
Rfree0.188 3617 Random
Rwork0.146 --
all0.148 --
obs-67533 -
Displacement parametersBiso mean: 16.47 Å2
Baniso -1Baniso -2Baniso -3
1--1.31 Å2-1.31 Å21.97 Å2
2---0.66 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error free: 0.0602 Å
Refinement stepCycle: LAST / Resolution: 1.45→56.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2498 0 129 474 3101
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.039
X-RAY DIFFRACTIONp_angle_deg2.931
X-RAY DIFFRACTIONp_improper_angle_d0.161
X-RAY DIFFRACTIONp_dihedral_angle_d4.632
LS refinement shellResolution: 1.45→1.488 Å
RfactorNum. reflection% reflection
Rfree0.298 241 -
Rwork0.203 --
obs-4882 99.7 %
Refinement
*PLUS
Lowest resolution: 95 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.039
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg4.632
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_improper_angle_deg0.161
LS refinement shell
*PLUS
Lowest resolution: 1.53 Å / % reflection Rfree: 241 % / Num. reflection Rwork: 4882

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