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

ID or keywords:

Entry

Database: PDB / ID: 2uum

Title

Crystal 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 BETA ...) x 2
C-PHYCOCYANIN ALPHA CHAIN

Keywords

ELECTRON TRANSPORT / PHOTOSYNTHESIS / SPIRULINA SP / C-PHYCOCYANIN / PHYCOBILISOME / MARINE / TRANSPORT / LYNGBYA SP / PHORMIDIUM / CHROMOPHORE / FRESH WATER / METHYLATION / BILE PIGMENT

Function / homology

Function and homology information

phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis
Similarity search - Function

Biological species

SPIRULINA SP. (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 3 Å

Authors

Satyanarayana, 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 Two Hexamers.
Authors: Satyanarayana, L. / Patel, A. / Mishra, S. / Ghosh, P.K. / Suresh, C.G.

History

Deposition	Mar 4, 2007	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 27, 2008	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Dec 13, 2023	Group: 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_ncs_dom_lim 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_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
Revision 1.4	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2uum.cif.gz	748.1 KB	Display	PDBx/mmCIF format
PDB format	pdb2uum.ent.gz	634.3 KB	Display	PDB format
PDBx/mmJSON format	2uum.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	2uum_validation.pdf.gz	9.7 MB	Display	wwPDB validaton report
Full document	2uum_full_validation.pdf.gz	10 MB	Display
Data in XML	2uum_validation.xml.gz	182 KB	Display
Data in CIF	2uum_validation.cif.gz	208.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uu/2uum ftp://data.pdbj.org/pub/pdb/validation_reports/uu/2uum	HTTPS FTP

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Related structure data

Related structure data	2uunC 1gh0S 2uul S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1ha7-2 2uul-1 2uun-2 1gh0-2 1gh0-1 2uun-1 4ziz-1 5o7m-1 5tou-d 6y3d-d 2uul-2 4h0m-2 4h0m-1 6jpr-d 1ha7-1 1ktp-2 1jbo-1 5mjm-1 5mjq-1 1i7y-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

2uunC

1gh0S

2uul

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

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

449 kDa, 24 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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

defined by author&software
225 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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

defined by author&software
225 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	107.332, 115.639, 183.258
Angle α, β, γ (deg.)	90.00, 90.03, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
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-ID	Ens-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	A	A	1 - 162	1 - 162
2	1	C	C	1 - 162	1 - 162
3	1	E	E	1 - 162	1 - 162
4	1	G	G	1 - 162	1 - 162
5	1	I	I	1 - 162	1 - 162
6	1	K	K	1 - 162	1 - 162
7	1	M	M	1 - 162	1 - 162
8	1	O	O	1 - 162	1 - 162
9	1	Q	Q	1 - 162	1 - 162
10	1	S	S	1 - 162	1 - 162
11	1	U	U	1 - 162	1 - 162
12	1	W	W	1 - 162	1 - 162
1	2	B	B	1 - 172	1 - 172
2	2	D	D	1 - 172	1 - 172
3	2	F	F	1 - 172	1 - 172
4	2	H	H	1 - 172	1 - 172
5	2	J	J	1 - 172	1 - 172
6	2	L	L	1 - 172	1 - 172
7	2	N	N	1 - 172	1 - 172
8	2	P	P	1 - 172	1 - 172
9	2	R	R	1 - 172	1 - 172
10	2	T	T	1 - 172	1 - 172
11	2	V	V	1 - 172	1 - 172
12	2	X	X	1 - 172	1 - 172

NCS ensembles :

ID
1
2

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Protein , 1 types, 12 molecules ACEGIKMOQSUW

#1: Protein	C-PHYCOCYANIN ALPHA CHAIN Mass: 17602.820 Da / Num. of mol.: 12 / Source method: isolated from a natural source Details: PHYCOCYANOBILIN ATTACHED ALFA-84 CYSTIENE RESIDUE AND BETA-82 AND 153 MONOMERS Source: (natural) SPIRULINA SP. (bacteria) / References: UniProt: P72509

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C-PHYCOCYANIN BETA ... , 2 types, 12 molecules BDFHJLNPRTVX

#2: Protein	C-PHYCOCYANIN BETA CHAIN Mass: 18080.496 Da / Num. of mol.: 11 / Source method: isolated from a natural source Details: PHYCOCYANOBILIN ATTACHED ALFA-84 CYSTIENE RESIDUE AND BETA-82 AND 153 MONOMERS. Source: (natural) SPIRULINA SP. (bacteria) / References: UniProt: P72508
#3: Protein	C-PHYCOCYANIN BETA CHAIN Mass: 18152.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: PHYCOCYANOBILIN ATTACHED ALFA-84 CYSTIENE RESIDUE AND BETA-82 AND 153 MONOMERS. Source: (natural) SPIRULINA SP. (bacteria) / References: UniProt: P72508

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Non-polymers , 3 types, 199 molecules

#4: Chemical	ChemComp-CYC / PHYCOCYANOBILIN Mass: 588.694 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₃₃H₄₀N₄O₆
#5: Chemical	... ChemComp-BLA / BILIVERDINE IX ALPHA Mass: 582.646 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C₃₃H₃₄N₄O₆
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has protein modification	Y
Sequence details	THE SPECIES FROM WHICH THE PROTEIN HAS BEEN EXTRACTED IS CURRENTLY UNKNOWN. IN THE PDB ENTRY IT HAS ...THE SPECIES FROM WHICH THE PROTEIN HAS BEEN EXTRACTED IS CURRENTLY UNKNOWN. IN THE PDB ENTRY IT HAS BEEN MATCHED TO SPIRULINA PLATENSIS WHICH HAS A SEQUENCE IDENTITY OF 98.14% (162 AMINO ACIDS) AND 97.674% (172 AMINO ACID CHAINS) AND HAS THE SAME GRANDPARENT IN THE TAXONOMY TREE.

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.5 Å³/Da / Density % sol: 50.6 % / Description: NONE
Crystal grow	pH: 6.5 Details: 0.01M SODIUM PHOSPHATE PH 6.5, 0.72 M SOD. FORMATE, AND 13.5% PEG 4K

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Data collection

Diffraction	Mean temperature: 110 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
Detector	Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Details: MIRRORS
Radiation	Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 3→40 Å / Num. obs: 86909 / % possible obs: 96.6 % / Observed criterion σ(I): 10 / Redundancy: 3 % / R_merge(I) obs: 0.09 / Net I/σ(I): 9.19
Reflection shell	Resolution: 3→3.11 Å / Redundancy: 2.3 % / R_merge(I) obs: 0.02 / Mean I/σ(I) obs: 3.9 / % possible all: 93.8

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
DENZO		data reduction
SCALEPACK		data scaling
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GH0

1gh0

Resolution: 3→182.57 Å / Cor.coef. F_o:F_c: 0.914 / Cor.coef. F_o:F_c free: 0.867 / SU B: 17.981 / SU ML: 0.333 / Cross valid method: THROUGHOUT / ESU R Free: 0.463 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.242	4331	5 %	RANDOM
R_work	0.201	-	-	-
obs	0.203	82635	96.5 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 25.03 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.46 Å²	0 Å²	0.13 Å²
2-	-	4.08 Å²	0 Å²
3-	-	-	-3.63 Å²

Refinement step

Cycle: LAST / Resolution: 3→182.57 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	29897	0	1548	163	31608

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.022	32003
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.378	2.023	43552
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.537	5	3984
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.315	24.095	1260
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.192	15	4912
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.018	15	204
X-RAY DIFFRACTION	r_chiral_restr	0.121	0.2	4813
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	24392
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.271	0.2	17031
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.32	0.2	22961
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.142	0.2	1027
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.475	0.2	177
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.348	0.2	12
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.645	1.5	20171
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.117	2	31571
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.367	3	24685
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	3.154	4.5	11981
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	1229	tight positional	0.08	0.05
1	2	C	1229	tight positional	0.09	0.05
1	3	E	1229	tight positional	0.08	0.05
1	4	G	1229	tight positional	0.08	0.05
1	5	I	1229	tight positional	0.08	0.05
1	6	K	1229	tight positional	0.09	0.05
1	7	M	1229	tight positional	0.09	0.05
1	8	O	1229	tight positional	0.09	0.05
1	9	Q	1229	tight positional	0.08	0.05
1	10	S	1229	tight positional	0.08	0.05
1	11	U	1229	tight positional	0.08	0.05
1	12	W	1229	tight positional	0.08	0.05
2	1	B	1254	tight positional	0.07	0.05
2	2	D	1254	tight positional	0.09	0.05
2	3	F	1254	tight positional	0.08	0.05
2	4	H	1254	tight positional	0.09	0.05
2	5	J	1254	tight positional	0.09	0.05
2	6	L	1254	tight positional	0.07	0.05
2	7	N	1254	tight positional	0.08	0.05
2	8	P	1254	tight positional	0.08	0.05
2	9	R	1254	tight positional	0.08	0.05
2	10	T	1254	tight positional	0.07	0.05
2	11	V	1254	tight positional	0.09	0.05
2	12	X	1254	tight positional	0.08	0.05
1	1	A	1229	tight thermal	0.16	0.5
1	2	C	1229	tight thermal	0.15	0.5
1	3	E	1229	tight thermal	0.15	0.5
1	4	G	1229	tight thermal	0.15	0.5
1	5	I	1229	tight thermal	0.16	0.5
1	6	K	1229	tight thermal	0.14	0.5
1	7	M	1229	tight thermal	0.17	0.5
1	8	O	1229	tight thermal	0.15	0.5
1	9	Q	1229	tight thermal	0.15	0.5
1	10	S	1229	tight thermal	0.15	0.5
1	11	U	1229	tight thermal	0.15	0.5
1	12	W	1229	tight thermal	0.15	0.5
2	1	B	1254	tight thermal	0.14	0.5
2	2	D	1254	tight thermal	0.15	0.5
2	3	F	1254	tight thermal	0.14	0.5
2	4	H	1254	tight thermal	0.15	0.5
2	5	J	1254	tight thermal	0.15	0.5
2	6	L	1254	tight thermal	0.15	0.5
2	7	N	1254	tight thermal	0.15	0.5
2	8	P	1254	tight thermal	0.14	0.5
2	9	R	1254	tight thermal	0.15	0.5
2	10	T	1254	tight thermal	0.15	0.5
2	11	V	1254	tight thermal	0.15	0.5
2	12	X	1254	tight thermal	0.16	0.5

LS refinement shell

Resolution: 3→3.08 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.313	321
R_work	0.256	5834

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Protein , 1 types, 12 molecules ACEGIKMOQSUW

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C-PHYCOCYANIN BETA ... , 2 types, 12 molecules BDFHJLNPRTVX

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Non-polymers , 3 types, 199 molecules

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-Protein , 1 types, 12 molecules ACEGIKMOQSUW

-C-PHYCOCYANIN BETA ... , 2 types, 12 molecules BDFHJLNPRTVX

-Non-polymers , 3 types, 199 molecules

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Protein , 1 types, 12 molecules ACEGIKMOQSUW

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C-PHYCOCYANIN BETA ... , 2 types, 12 molecules BDFHJLNPRTVX

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Non-polymers , 3 types, 199 molecules

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Experimental details

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