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Basic information

Entry
Database: PDB / ID: 1cpc
TitleISOLATION, CRYSTALLIZATION, CRYSTAL STRUCTURE ANALYSIS AND REFINEMENT OF CONSTITUTIVE C-PHYCOCYANIN FROM THE CHROMATICALLY ADAPTING CYANOBACTERIUM FREMYELLA DIPLOSIPHON AT 1.66 ANGSTROMS RESOLUTION
Components
  • C-PHYCOCYANIN (ALPHA SUBUNIT)
  • C-PHYCOCYANIN (BETA SUBUNIT)
KeywordsLIGHT HARVESTING PROTEIN
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-1 beta subunit / C-phycocyanin-1 alpha subunit
Similarity search - Component
Biological speciesFremyella diplosiphon (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.66 Å
AuthorsDuerring, M. / Schmidt, G.B. / Huber, R.
CitationJournal: J.Mol.Biol. / Year: 1991
Title: Isolation, crystallization, crystal structure analysis and refinement of constitutive C-phycocyanin from the chromatically adapting cyanobacterium Fremyella diplosiphon at 1.66 A resolution.
Authors: Duerring, M. / Schmidt, G.B. / Huber, R.
History
DepositionOct 11, 1990Processing site: BNL
Revision 1.0Jan 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 10, 2013Group: Non-polymer description / Structure summary
Revision 1.4Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _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_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 SUBUNIT)
B: C-PHYCOCYANIN (BETA SUBUNIT)
K: C-PHYCOCYANIN (ALPHA SUBUNIT)
L: C-PHYCOCYANIN (BETA SUBUNIT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,91910
Polymers70,3874
Non-polymers3,5326
Water4,378243
1
A: C-PHYCOCYANIN (ALPHA SUBUNIT)
B: C-PHYCOCYANIN (BETA SUBUNIT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9605
Polymers35,1942
Non-polymers1,7663
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6620 Å2
ΔGint-74 kcal/mol
Surface area14800 Å2
MethodPISA
2
K: C-PHYCOCYANIN (ALPHA SUBUNIT)
L: C-PHYCOCYANIN (BETA SUBUNIT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9605
Polymers35,1942
Non-polymers1,7663
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6610 Å2
ΔGint-75 kcal/mol
Surface area14760 Å2
MethodPISA
3
A: C-PHYCOCYANIN (ALPHA SUBUNIT)
B: C-PHYCOCYANIN (BETA SUBUNIT)
K: C-PHYCOCYANIN (ALPHA SUBUNIT)
L: C-PHYCOCYANIN (BETA SUBUNIT)
hetero molecules

A: C-PHYCOCYANIN (ALPHA SUBUNIT)
B: C-PHYCOCYANIN (BETA SUBUNIT)
K: C-PHYCOCYANIN (ALPHA SUBUNIT)
L: C-PHYCOCYANIN (BETA SUBUNIT)
hetero molecules

A: C-PHYCOCYANIN (ALPHA SUBUNIT)
B: C-PHYCOCYANIN (BETA SUBUNIT)
K: C-PHYCOCYANIN (ALPHA SUBUNIT)
L: C-PHYCOCYANIN (BETA SUBUNIT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,75830
Polymers211,16212
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
Buried area61450 Å2
ΔGint-537 kcal/mol
Surface area66930 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

A: C-PHYCOCYANIN (ALPHA SUBUNIT)
B: C-PHYCOCYANIN (BETA SUBUNIT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,87915
Polymers105,5816
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 area24680 Å2
ΔGint-260 kcal/mol
Surface area39610 Å2
MethodPISA
5
K: C-PHYCOCYANIN (ALPHA SUBUNIT)
L: C-PHYCOCYANIN (BETA SUBUNIT)
hetero molecules

K: C-PHYCOCYANIN (ALPHA SUBUNIT)
L: C-PHYCOCYANIN (BETA SUBUNIT)
hetero molecules

K: C-PHYCOCYANIN (ALPHA SUBUNIT)
L: C-PHYCOCYANIN (BETA SUBUNIT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,87915
Polymers105,5816
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 area24630 Å2
ΔGint-260 kcal/mol
Surface area39460 Å2
MethodPISA
6


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16460 Å2
ΔGint-152 kcal/mol
Surface area26340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.260, 180.260, 61.240
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein C-PHYCOCYANIN (ALPHA SUBUNIT)


Mass: 17243.271 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fremyella diplosiphon (bacteria) / Genus: Microchaete / References: UniProt: P07122
#2: Protein C-PHYCOCYANIN (BETA SUBUNIT)


Mass: 17950.377 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fremyella diplosiphon (bacteria) / Genus: Microchaete / References: UniProt: P07119
#3: Chemical
ChemComp-CYC / PHYCOCYANOBILIN


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


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.79 %
Crystal grow
*PLUS
pH: 5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein1drop
211 %PEG1reservior
30.1 Mphosphate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.66 Å / Num. obs: 70981 / Num. measured all: 176017 / Rmerge(I) obs: 0.089
Reflection shell
*PLUS
Highest resolution: 1.66 Å / Lowest resolution: 1.75 Å / % possible obs: 29.1 %

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Processing

SoftwareName: EREF / Classification: refinement
RefinementRfactor Rwork: 0.181 / Highest resolution: 1.66 Å
Refinement stepCycle: LAST / Highest resolution: 1.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4933 0 258 243 5434
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.016
X-RAY DIFFRACTIONo_angle_deg2.33
Software
*PLUS
Name: EREF / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å / Rfactor Rwork: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: o_angle_d / Dev ideal: 2.33

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