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- PDB-1gh0: CRYSTAL STRUCTURE OF C-PHYCOCYANIN FROM SPIRULINA PLATENSIS -

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Basic information

Entry
Database: PDB / ID: 1gh0
TitleCRYSTAL STRUCTURE OF C-PHYCOCYANIN FROM SPIRULINA PLATENSIS
Components
  • C-PHYCOCYANIN ALPHA SUBUNIT
  • C-PHYCOCYANIN BETA SUBUNIT
KeywordsPHOTOSYNTHESIS / C-phycocyanin from Spirulina platensis
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 speciesArthrospira platensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsLiang, D.-C. / Chang, W.-R. / Wang, X.-Q.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structure of C-phycocyanin from Spirulina platensis at 2.2 A resolution: a novel monoclinic crystal form for phycobiliproteins in phycobilisomes.
Authors: Wang, X.Q. / Li, L.N. / Chang, W.R. / Zhang, J.P. / Gui, L.L. / Guo, B.J. / Liang, D.C.
History
DepositionOct 29, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.type
Revision 1.4Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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_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
C: C-PHYCOCYANIN ALPHA SUBUNIT
D: C-PHYCOCYANIN BETA SUBUNIT
E: C-PHYCOCYANIN ALPHA SUBUNIT
F: C-PHYCOCYANIN BETA SUBUNIT
G: C-PHYCOCYANIN ALPHA SUBUNIT
H: C-PHYCOCYANIN BETA SUBUNIT
I: C-PHYCOCYANIN ALPHA SUBUNIT
J: C-PHYCOCYANIN BETA SUBUNIT
K: C-PHYCOCYANIN ALPHA SUBUNIT
L: C-PHYCOCYANIN BETA SUBUNIT
M: C-PHYCOCYANIN ALPHA SUBUNIT
N: C-PHYCOCYANIN BETA SUBUNIT
O: C-PHYCOCYANIN ALPHA SUBUNIT
P: C-PHYCOCYANIN BETA SUBUNIT
Q: C-PHYCOCYANIN ALPHA SUBUNIT
R: C-PHYCOCYANIN BETA SUBUNIT
S: C-PHYCOCYANIN ALPHA SUBUNIT
T: C-PHYCOCYANIN BETA SUBUNIT
U: C-PHYCOCYANIN ALPHA SUBUNIT
V: C-PHYCOCYANIN BETA SUBUNIT
W: C-PHYCOCYANIN ALPHA SUBUNIT
X: C-PHYCOCYANIN BETA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)449,48960
Polymers428,29624
Non-polymers21,19336
Water17,024945
1
A: C-PHYCOCYANIN ALPHA SUBUNIT
B: C-PHYCOCYANIN BETA SUBUNIT
C: C-PHYCOCYANIN ALPHA SUBUNIT
D: C-PHYCOCYANIN BETA SUBUNIT
E: C-PHYCOCYANIN ALPHA SUBUNIT
F: C-PHYCOCYANIN BETA SUBUNIT
G: C-PHYCOCYANIN ALPHA SUBUNIT
H: C-PHYCOCYANIN BETA SUBUNIT
I: C-PHYCOCYANIN ALPHA SUBUNIT
J: C-PHYCOCYANIN BETA SUBUNIT
K: C-PHYCOCYANIN ALPHA SUBUNIT
L: C-PHYCOCYANIN BETA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,74530
Polymers214,14812
Non-polymers10,59618
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area61900 Å2
ΔGint-546 kcal/mol
Surface area68190 Å2
MethodPISA
2
M: C-PHYCOCYANIN ALPHA SUBUNIT
N: C-PHYCOCYANIN BETA SUBUNIT
O: C-PHYCOCYANIN ALPHA SUBUNIT
P: C-PHYCOCYANIN BETA SUBUNIT
Q: C-PHYCOCYANIN ALPHA SUBUNIT
R: C-PHYCOCYANIN BETA SUBUNIT
S: C-PHYCOCYANIN ALPHA SUBUNIT
T: C-PHYCOCYANIN BETA SUBUNIT
U: C-PHYCOCYANIN ALPHA SUBUNIT
V: C-PHYCOCYANIN BETA SUBUNIT
W: C-PHYCOCYANIN ALPHA SUBUNIT
X: C-PHYCOCYANIN BETA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,74530
Polymers214,14812
Non-polymers10,59618
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area61830 Å2
ΔGint-550 kcal/mol
Surface area68160 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area125000 Å2
ΔGint-1103 kcal/mol
Surface area135090 Å2
MethodPISA
4
A: C-PHYCOCYANIN ALPHA SUBUNIT
B: C-PHYCOCYANIN BETA SUBUNIT
C: C-PHYCOCYANIN ALPHA SUBUNIT
D: C-PHYCOCYANIN BETA SUBUNIT
E: C-PHYCOCYANIN ALPHA SUBUNIT
F: C-PHYCOCYANIN BETA SUBUNIT
G: C-PHYCOCYANIN ALPHA SUBUNIT
H: C-PHYCOCYANIN BETA SUBUNIT
I: C-PHYCOCYANIN ALPHA SUBUNIT
J: C-PHYCOCYANIN BETA SUBUNIT
K: C-PHYCOCYANIN ALPHA SUBUNIT
L: C-PHYCOCYANIN BETA SUBUNIT
hetero molecules

M: C-PHYCOCYANIN ALPHA SUBUNIT
N: C-PHYCOCYANIN BETA SUBUNIT
O: C-PHYCOCYANIN ALPHA SUBUNIT
P: C-PHYCOCYANIN BETA SUBUNIT
Q: C-PHYCOCYANIN ALPHA SUBUNIT
R: C-PHYCOCYANIN BETA SUBUNIT
S: C-PHYCOCYANIN ALPHA SUBUNIT
T: C-PHYCOCYANIN BETA SUBUNIT
U: C-PHYCOCYANIN ALPHA SUBUNIT
V: C-PHYCOCYANIN BETA SUBUNIT
W: C-PHYCOCYANIN ALPHA SUBUNIT
X: C-PHYCOCYANIN BETA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)449,48960
Polymers428,29624
Non-polymers21,19336
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area125570 Å2
ΔGint-1107 kcal/mol
Surface area134520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.0, 117.5, 185.0
Angle α, β, γ (deg.)90.0, 90.3, 90.0
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
C-PHYCOCYANIN ALPHA SUBUNIT


Mass: 17602.820 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Arthrospira platensis (bacteria) / References: UniProt: P72509
#2: Protein
C-PHYCOCYANIN BETA SUBUNIT


Mass: 18088.520 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Arthrospira platensis (bacteria) / References: UniProt: P72508
#3: Chemical...
ChemComp-CYC / PHYCOCYANOBILIN / Phycocyanobilin


Mass: 588.694 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: C33H40N4O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 945 / 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: 2.77 Å3/Da / Density % sol: 55.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion/hanging drop / pH: 6.8
Details: pH 6.8, vapour diffusion/hanging drop, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16.5 mg/mlprotein1drop
2100 mMphosphate1drop
38 %(v/v)satammonium sulfate1drop
43 %(v/v)sat1dropNaCl
51.25 %(v/v)MPD1drop
625 %(v/v)satammonium sulfate1reservoir
7100 mMphosphate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Type: PHOTON FACTORY / Wavelength: 1
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 296302 / % possible obs: 94.5 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 10.1
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.61 / Num. unique all: 18524 / % possible all: 88.8
Reflection
*PLUS
% possible obs: 95.4 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.075
Reflection shell
*PLUS
% possible obs: 94.4 % / Num. unique obs: 14756 / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 2.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementResolution: 2.2→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.237 9858 -
Rwork0.189 --
obs-215682 91.4 %
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30000 0 1548 945 32493
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.1
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg20.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.7
LS refinement shell
*PLUS
Rfactor Rfree: 0.291 / Num. reflection obs: 14756 / Rfactor obs: 0.257

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