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- PDB-2uul: Crystal structure of C-phycocyanin from Phormidium, Lyngbya spp. ... -

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Basic information

Entry
Database: PDB / ID: 2uul
TitleCrystal structure of C-phycocyanin from Phormidium, Lyngbya spp. (Marine) and Spirulina sp. (Fresh water) shows two different ways of energy transfer between two hexamers.
Components
  • (C-PHYCOCYANIN ALPHA ...) x 2
  • (C-PHYCOCYANIN BETA ...) x 3
KeywordsELECTRON TRANSPORT / C-PHYCOCYANIN / PHYCOBILISOME / PHOTOSYNTHESIS / CHROMOPHORE / FRESH WATER / METHYLATION / BILE PIGMENT / MARINE / LYNGBYA / SPIRULINA / TRANSPORT / PHORMIDIUM
Function / homologyPhycocyanins / Globin-like / Orthogonal Bundle / Mainly Alpha / BILIVERDINE IX ALPHA / PHYCOCYANOBILIN
Function and homology information
Biological speciesPHORMIDIUM SP. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsSatyanarayana, L. / Patel, A. / Mishra, S. / K Ghosh, P. / Suresh, C.G.
Citation
Journal: To be Published
Title: Crystal Structure of C-Phycocyanin from Phormidium, Lyngbya Spp. (Marine) and Spirulina Sp. (Fresh Water) Shows Two Different Ways of Energy Transfer between Twohexamers.
Authors: Satyanarayana, L. / Patel, A. / Mishra, S. / Ghosh, P.K. / Suresh, C.G.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2005
Title: X-Ray Crystallographic Studies on C-Phycocyanins from Cyanobacteria from Different Habitats: Marine and Freshwater.
Authors: Satyanarayana, L. / Suresh, C.G. / Patel, A. / Mishra, S. / Ghosh, P.K.
#2: Journal: Protein Expr.Purif. / Year: 2005
Title: Purification and Charactarization of C-Phycocyanin from Cyanobacterial Species of Marine and Freshwater Habitat.
Authors: Patel, A. / Mishra, S. / Pawar, R. / Ghosh, P.K.
History
DepositionMar 4, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C-PHYCOCYANIN ALPHA CHAIN
B: C-PHYCOCYANIN BETA CHAIN
C: C-PHYCOCYANIN ALPHA CHAIN
D: C-PHYCOCYANIN BETA CHAIN
E: C-PHYCOCYANIN ALPHA CHAIN
F: C-PHYCOCYANIN BETA CHAIN
G: C-PHYCOCYANIN ALPHA CHAIN
H: C-PHYCOCYANIN BETA CHAIN
I: C-PHYCOCYANIN ALPHA CHAIN
J: C-PHYCOCYANIN BETA CHAIN
K: C-PHYCOCYANIN ALPHA CHAIN
L: C-PHYCOCYANIN BETA CHAIN
M: C-PHYCOCYANIN ALPHA CHAIN
N: C-PHYCOCYANIN BETA CHAIN
O: C-PHYCOCYANIN ALPHA CHAIN
P: C-PHYCOCYANIN BETA CHAIN
Q: C-PHYCOCYANIN ALPHA CHAIN
R: C-PHYCOCYANIN BETA CHAIN
S: C-PHYCOCYANIN ALPHA CHAIN
T: C-PHYCOCYANIN BETA CHAIN
U: C-PHYCOCYANIN ALPHA CHAIN
V: C-PHYCOCYANIN BETA CHAIN
W: C-PHYCOCYANIN ALPHA CHAIN
X: C-PHYCOCYANIN BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)443,04960
Polymers421,87424
Non-polymers21,17536
Water2,504139
1
A: C-PHYCOCYANIN ALPHA CHAIN
B: C-PHYCOCYANIN BETA CHAIN
C: C-PHYCOCYANIN ALPHA CHAIN
D: C-PHYCOCYANIN BETA CHAIN
E: C-PHYCOCYANIN ALPHA CHAIN
F: C-PHYCOCYANIN BETA CHAIN
G: C-PHYCOCYANIN ALPHA CHAIN
H: C-PHYCOCYANIN BETA CHAIN
I: C-PHYCOCYANIN ALPHA CHAIN
J: C-PHYCOCYANIN BETA CHAIN
K: C-PHYCOCYANIN ALPHA CHAIN
L: C-PHYCOCYANIN BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,58030
Polymers211,00112
Non-polymers10,57818
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31670 Å2
ΔGint-591.5 kcal/mol
Surface area95470 Å2
MethodPQS
2
M: C-PHYCOCYANIN ALPHA CHAIN
N: C-PHYCOCYANIN BETA CHAIN
O: C-PHYCOCYANIN ALPHA CHAIN
P: C-PHYCOCYANIN BETA CHAIN
Q: C-PHYCOCYANIN ALPHA CHAIN
R: C-PHYCOCYANIN BETA CHAIN
S: C-PHYCOCYANIN ALPHA CHAIN
T: C-PHYCOCYANIN BETA CHAIN
U: C-PHYCOCYANIN ALPHA CHAIN
V: C-PHYCOCYANIN BETA CHAIN
W: C-PHYCOCYANIN ALPHA CHAIN
X: C-PHYCOCYANIN BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,47030
Polymers210,87312
Non-polymers10,59618
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38810 Å2
ΔGint-326.1 kcal/mol
Surface area103940 Å2
MethodPQS
Unit cell
Length a, b, c (Å)107.878, 115.783, 183.549
Angle α, β, γ (deg.)90.00, 90.24, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41G
51I
61K
71M
81O
91Q
101S
111U
121W
12B
22D
32F
42H
52J
62L
72N
82P
92R
102T
112V
122X

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 1

Dom-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA1 - 1621 - 162
21CC1 - 1621 - 162
31EE1 - 1621 - 162
41GG1 - 1621 - 162
51II1 - 1621 - 162
61KK1 - 1621 - 162
71MM1 - 1621 - 162
81OO1 - 1621 - 162
91QQ1 - 1621 - 162
101SS1 - 1621 - 162
111UU1 - 1621 - 162
121WW1 - 1621 - 162
12BB1 - 1721 - 172
22DD1 - 1721 - 172
32FF1 - 1721 - 172
42HH1 - 1721 - 172
52JJ1 - 1721 - 172
62LL1 - 1721 - 172
72NN1 - 1721 - 172
82PP1 - 1721 - 172
92RR1 - 1721 - 172
102TT1 - 1721 - 172
112VV1 - 1721 - 172
122XX1 - 1721 - 172

NCS ensembles :
ID
1
2

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Components

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C-PHYCOCYANIN ALPHA ... , 2 types, 12 molecules AEGIKMOQSUWC

#1: Protein
C-PHYCOCYANIN ALPHA CHAIN


Mass: 17318.387 Da / Num. of mol.: 11 / Source method: isolated from a natural source
Details: PHYCOCYANOBILIN ATTACHED ALFA-84 CYSTEINE RESIDUE AND BETA-82 AND 153 MONOMERS
Source: (natural) PHORMIDIUM SP. (bacteria)
#3: Protein C-PHYCOCYANIN ALPHA CHAIN


Mass: 17362.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: PHYCOCYANOBILIN ATTACHED ALFA-84 CYSTEINE RESIDUE AND BETA-82 AND 153 MONOMERS, RESIDUE 143 IS SER IN CHAIN C WHERE AS IT IS ALA IN OTHER CHAINS
Source: (natural) PHORMIDIUM SP. (bacteria)

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C-PHYCOCYANIN BETA ... , 3 types, 12 molecules BFJLNPRTVXDH

#2: Protein
C-PHYCOCYANIN BETA CHAIN


Mass: 17827.139 Da / Num. of mol.: 10 / Source method: isolated from a natural source
Details: PHYCOCYANOBILIN ATTACHED ALFA-84 CYSTEINE RESIDUE AND BETA-82 AND 153 MONOMERS
Source: (natural) PHORMIDIUM SP. (bacteria)
#4: Protein C-PHYCOCYANIN BETA CHAIN


Mass: 17959.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: PHYCOCYANOBILIN ATTACHED ALFA-84 CYSTEINE RESIDUE AND BETA-82 AND 153 MONOMERS, RESIDUES 9 AND 10 ARE VAL SER IN THIS CHAIN WHEREAS IT IS ALA ALA IN OTHER CHAINS
Source: (natural) PHORMIDIUM SP. (bacteria)
#5: Protein C-PHYCOCYANIN BETA CHAIN


Mass: 17779.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: PHYCOCYANOBILIN ATTACHED ALFA-84 CYSTEINE RESIDUE AND BETA-82 AND 153 MONOMERS, RESIDUE 74 IS ASP IN THIS CHAIN WHERE AS IT IS TYR IN OTHER CHAINS
Source: (natural) PHORMIDIUM SP. (bacteria)

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Non-polymers , 3 types, 175 molecules

#6: Chemical...
ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: C33H40N4O6
#7: Chemical ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C33H34N4O6
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE SPECIES FROM WHICH THE PROTEIN HAS BEEN EXTRACTED IS CURRENTLY UNKNOWN. THIS PDB ENTRY HAS BEEN ...THE SPECIES FROM WHICH THE PROTEIN HAS BEEN EXTRACTED IS CURRENTLY UNKNOWN. THIS PDB ENTRY HAS BEEN MAPPED AGAINST ITSELF. THE ONLY KNOWN FACT IS THE GRANDPARENT IN THE TAXONOMY TREE, WHICH IS CYANOBACTERIA FOR THIS ENTRY AND THE GENUS IS PHORMIDIUM SP.

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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: 2.51 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growpH: 6.5
Details: 0.01M SODIUM PHOSPHATE PH 6.5, 0.72M SOD. FORMATE, 9%PEG 1K AND 9% PEG 8K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. obs: 82067 / % possible obs: 96.6 % / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 5.27
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.03 / Mean I/σ(I) obs: 2.46 / % possible all: 93.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GH0

1gh0


Resolution: 3.1→25 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.85 / SU B: 19.91 / SU ML: 0.354 / Cross valid method: THROUGHOUT / ESU R Free: 0.521 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.245 3825 5 %RANDOM
Rwork0.2 ---
obs0.202 72183 92.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å20 Å2-0.63 Å2
2--3.13 Å20 Å2
3----2.19 Å2
Refinement stepCycle: LAST / Resolution: 3.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29444 0 1548 139 31131
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.02231543
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.5122.01442993
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.04853984
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.32824.1031260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.342154580
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.66115204
X-RAY DIFFRACTIONr_chiral_restr0.1310.24744
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0224284
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2880.216659
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.21063
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4450.2132
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4170.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6871.520164
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.181231308
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.492324274
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4014.511685
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1200tight positional0.10.05
12C1200tight positional0.080.05
13E1200tight positional0.10.05
14G1200tight positional0.090.05
15I1200tight positional0.090.05
16K1200tight positional0.090.05
17M1200tight positional0.080.05
18O1200tight positional0.080.05
19Q1200tight positional0.090.05
110S1200tight positional0.10.05
111U1200tight positional0.090.05
112W1200tight positional0.080.05
21B1201tight positional0.090.05
22D1201tight positional0.080.05
23F1201tight positional0.080.05
24H1201tight positional0.080.05
25J1201tight positional0.070.05
26L1201tight positional0.080.05
27N1201tight positional0.090.05
28P1201tight positional0.080.05
29R1201tight positional0.090.05
210T1201tight positional0.080.05
211V1201tight positional0.090.05
212X1201tight positional0.080.05
11A1200tight thermal0.140.5
12C1200tight thermal0.140.5
13E1200tight thermal0.160.5
14G1200tight thermal0.140.5
15I1200tight thermal0.160.5
16K1200tight thermal0.140.5
17M1200tight thermal0.150.5
18O1200tight thermal0.150.5
19Q1200tight thermal0.160.5
110S1200tight thermal0.170.5
111U1200tight thermal0.140.5
112W1200tight thermal0.150.5
21B1201tight thermal0.140.5
22D1201tight thermal0.140.5
23F1201tight thermal0.140.5
24H1201tight thermal0.140.5
25J1201tight thermal0.140.5
26L1201tight thermal0.140.5
27N1201tight thermal0.150.5
28P1201tight thermal0.130.5
29R1201tight thermal0.150.5
210T1201tight thermal0.140.5
211V1201tight thermal0.160.5
212X1201tight thermal0.130.5
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.319 230
Rwork0.26 4369

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