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- PDB-1on7: Unmethylated form of C-phycocyanin from Themosynechococcus vulcan... -

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Basic information

Entry
Database: PDB / ID: 1on7
TitleUnmethylated form of C-phycocyanin from Themosynechococcus vulcanus at 2.7A
Components
  • C-phycocyanin alpha subunit
  • C-phycocyanin beta subunit
KeywordsPHOTOSYNTHESIS / antenna / phycobilisome / cyanobacteria
Function / homology
Function and homology information


phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis
Similarity search - Function
Phycocyanin, alpha subunit / Phycocyanins / Phycocyanin, beta subunit / 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: 2.7 Å
AuthorsAdir, N. / Lerner, N.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: The crystal structure of a novel unmethylated form of C-phycocyanin, a possible connector between cores and rods in pycobilisomes
Authors: Adir, N. / Lerner, N.
History
DepositionFeb 27, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)37,4395
Polymers35,6732
Non-polymers1,7663
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6620 Å2
ΔGint-67 kcal/mol
Surface area14590 Å2
MethodPISA
2
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)112,31815
Polymers107,0206
Non-polymers5,2989
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_535-y,x-y-2,z1
crystal symmetry operation3_755-x+y+2,-x,z1
Buried area24820 Å2
ΔGint-241 kcal/mol
Surface area38820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.290, 153.290, 39.048
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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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 / Details: Phycobilisome / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: Q9AM02
#2: Protein C-phycocyanin beta subunit


Mass: 18202.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Phycobilisome / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: Q71RW8
#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.: 36 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.55 Å3/Da / Density % sol: 65.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG4000, Bis-Tris, 6.3mg/ml protein, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mMHEPES1droppH8.0
220 mg/mlprotein1drop
36.7 %PEG40001drop
46.3 mg/mlPC6121drop
570 mMBis-Tris1droppH7.0
610 %PEG40001reservoir
7100 mMbis-Tris1reservoirpH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8126 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8126 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 13165 / Num. obs: 12540 / % possible obs: 84.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 54.2 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 7.4
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.2 / Num. unique all: 1036 / % possible all: 70.2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KTP

1ktp


Resolution: 2.7→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.278 1000 RANDOM
Rwork0.209 --
all-10088 -
obs-9088 -
Displacement parametersBiso mean: 50.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2499 0 129 36 2664
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.0085
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.26
LS refinement shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 2.8 Å / Rfactor Rfree: 0.32 / Rfactor Rwork: 0.346

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