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- PDB-3o18: Crystal structure of c-phycocyanin from Themosynechococcus vulcan... -

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Basic information

Entry
Database: PDB / ID: 3o18
TitleCrystal structure of c-phycocyanin from Themosynechococcus vulcanus at 1.35 angstroms resolution
Components
  • C-phycocyanin alpha subunit
  • C-phycocyanin beta subunit
KeywordsPHOTOSYNTHESIS / Phycobilisome / Light Harvesting / Cyanobacteria
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 / Resolution: 1.35 Å
AuthorsMarx, A. / David, L. / 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 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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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
Water7,224401
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 area24250 Å2
ΔGint-237 kcal/mol
Surface area39770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.807, 186.807, 59.822
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
DetailsThe phycocyanin hexamer is part of a larger multicomponent 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.: 401 / 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: 2.81 Å3/Da / Density % sol: 56.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.8M Ammonium sulfate, 10.5% sucrose, 50mM Tris , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / 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: 1.35→93.404 Å / Num. obs: 86032 / % possible obs: 99 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 13.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
1.35-1.425.40.4361.7120840.43695.6
1.42-1.518.60.3062.4119270.30699.9
1.51-1.6110.60.2133.4112680.213100
1.61-1.7410.30.1584.5104790.158100
1.74-1.919.80.1195.896270.119100
1.91-2.139.20.0877.287600.087100

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KTP

1ktp


Resolution: 1.35→27.23 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 0.001 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2263 4325 5 %RANDOM
Rwork0.2098 ---
obs0.2106 86029 98.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 60.24 Å2 / Biso mean: 20.8737 Å2 / Biso min: 10.33 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å2-0.35 Å20 Å2
2---0.69 Å20 Å2
3---1.04 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.35→27.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2500 0 129 401 3030
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013662
X-RAY DIFFRACTIONc_angle_d1.28014
X-RAY DIFFRACTIONc_dihedral_angle_d19.24167
X-RAY DIFFRACTIONc_improper_angle_d1.22596
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 324 -
Rwork0.286 5639 -
all-5963 -
obs--92.9 %

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