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- PDB-1ktp: Crystal structure of c-phycocyanin of synechococcus vulcanus at 1... -

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Basic information

Entry
Database: PDB / ID: 1ktp
TitleCrystal structure of c-phycocyanin of synechococcus vulcanus at 1.6 angstroms
Components
  • C-PHYCOCYANIN ALPHA SUBUNIT
  • C-PHYCOCYANIN BETA SUBUNIT
KeywordsPHOTOSYNTHESIS / CYANOBACTERIA / PHOTOSYSTEM II / LIGHT HARVESTING PROTEINS / THERMOSTABILITY
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 speciesThermosynechococcus vulcanus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsAdir, N. / Dobrovetsky, E. / Lerner, N.
CitationJournal: Biochim.Biophys.Acta / Year: 2002
Title: Refined structure of c-phycocyanin from the cyanobacterium Synechococcus vulcanus at 1.6 A: insights into the role of solvent molecules in thermal stability and co-factor structure
Authors: Adir, N. / Vainer, R. / Lerner, N.
History
DepositionJan 17, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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
Revision 2.0Mar 12, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / struct_asym / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_asym.entity_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_site.details / _struct_site.pdbx_auth_comp_id

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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)37,4535
Polymers35,6872
Non-polymers1,7663
Water6,792377
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6510 Å2
ΔGint-70 kcal/mol
Surface area14650 Å2
MethodPISA
2
A: C-PHYCOCYANIN ALPHA SUBUNIT
B: C-PHYCOCYANIN BETA SUBUNIT
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)224,72030
Polymers214,12412
Non-polymers10,59618
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_675x-y+1,-y+2,-z1
crystal symmetry operation6_765-x+2,-x+y+1,-z1
Buried area60680 Å2
ΔGint-528 kcal/mol
Surface area66260 Å2
MethodPISA
3
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_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area24370 Å2
ΔGint-243 kcal/mol
Surface area39100 Å2
MethodPISA
4
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)74,90710
Polymers71,3754
Non-polymers3,5326
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area16170 Å2
ΔGint-149 kcal/mol
Surface area26140 Å2
MethodPISA
5
B: C-PHYCOCYANIN BETA SUBUNIT
hetero molecules

B: C-PHYCOCYANIN BETA SUBUNIT
hetero molecules

A: C-PHYCOCYANIN ALPHA SUBUNIT
hetero molecules

A: C-PHYCOCYANIN ALPHA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,90710
Polymers71,3754
Non-polymers3,5326
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
crystal symmetry operation5_675x-y+1,-y+2,-z1
Buried area11000 Å2
ΔGint-106 kcal/mol
Surface area31310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.346, 186.346, 59.260
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein C-PHYCOCYANIN ALPHA SUBUNIT


Mass: 17470.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus vulcanus (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: P50032
#2: Protein C-PHYCOCYANIN BETA SUBUNIT


Mass: 18216.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus vulcanus (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.: 377 / 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: 2.35 Å3/Da / Density % sol: 55.65 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 5% PEG4000, 50MM HEPES, 5MG/ML PROTEIN, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 8 / Details: Adir, N., (2001) J. Mol. Biol., 313, 71.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 %PEG40001drop
250 mMTris1drop
32.5-5 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.928
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 16, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.928 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. all: 47823 / Num. obs: 47798 / % possible obs: 92.6 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 26.3 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 10
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3 / % possible all: 87.4
Reflection
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 20 Å / Num. obs: 51656 / % possible obs: 97.5 % / Redundancy: 5.6 % / Num. measured all: 419135 / Rmerge(I) obs: 0.078
Reflection shell
*PLUS
% possible obs: 99.3 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I7Y

1i7y


Resolution: 1.6→20 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.247 3977 7.7 %RANDOM
Rwork0.216 ---
obs0.216 39609 76.8 %-
Displacement parametersBiso mean: 21.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.17 Å
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2500 0 129 377 3006
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.22
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.16
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.6→1.66 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3161 263 10.8 %
Rwork0.28 2188 -
obs--47.8 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 20 Å / Num. reflection obs: 35632 / % reflection Rfree: 7.7 % / Rfactor obs: 0.212 / Rfactor Rfree: 0.254
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.06
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg17.16
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83
LS refinement shell
*PLUS
Rfactor Rfree: 0.3195 / % reflection Rfree: 10.8 % / Rfactor Rwork: 0.28 / Num. reflection obs: 3977 / Rfactor obs: 0.302

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