1GH0

CRYSTAL STRUCTURE OF C-PHYCOCYANIN FROM SPIRULINA PLATENSIS

PDB DOI: https://doi.org/10.2210/pdb1GH0/pdb

Classification: PHOTOSYNTHESIS
Organism(s): Arthrospira platensis
Mutation(s): Yes

Deposited: 2000-10-29 Released: 2001-06-06
Deposition Author(s): Liang, D.-C., Chang, W.-R., Wang, X.-Q.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.237
R-Value Work: 0.189

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Structure of C-phycocyanin from Spirulina platensis at 2.2 A resolution: a novel monoclinic crystal form for phycobiliproteins in phycobilisomes.

Wang, X.Q., Li, L.N., Chang, W.R., Zhang, J.P., Gui, L.L., Guo, B.J., Liang, D.C.

(2001) Acta Crystallogr D Biol Crystallogr 57: 784-792

PubMed: 11375497 Search on PubMed
DOI: https://doi.org/10.1107/s0907444901004528
Primary Citation of Related Structures:
1GH0

PubMed Abstract:
The crystal structure of C-phycocyanin from the cyanobacterium S. platensis has been determined at 2.2 A resolution. The crystals belong to the monoclinic crystal form, which has not been previously reported for phycobiliprotein structures. The structure was solved using the molecular-replacement method with a final R value of 18.9% (R(free) = 23.7%) after model building and refinement. In the crystals used for the study, the C-phycocyanin hexamers formed by face-to-face association of two trimers are arranged in layers rather than in columns. Three different kinds of packing between adjacent hexamers in the layer were compared. The tight packing of two adjacent hexamers formed by four trimers in the asymmetric unit brings beta155 PCB chromophores close together, so it is possible that lateral energy transfer takes place through the beta155-beta155 route.

Organizational Affiliation

National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, People's Republic of China.

Macromolecule Content

Total Structure Weight: 449.49 kDa
Atom Count: 32,493
Modelled Residue Count: 4,008
Deposited Residue Count: 4,008
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C-PHYCOCYANIN ALPHA SUBUNIT	A, C, E, G, I A, C, E, G, I, K, M, O, Q, S, U, W	162	Arthrospira platensis	Mutation(s): 0
UniProt
Find proteins for P72509 (Arthrospira platensis) Explore P72509 Go to UniProtKB: P72509
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P72509
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
C-PHYCOCYANIN BETA SUBUNIT	B, D, F, H, J B, D, F, H, J, L, N, P, R, T, V, X	172	Arthrospira platensis	Mutation(s): 1
UniProt
Find proteins for P72508 (Arthrospira platensis) Explore P72508 Go to UniProtKB: P72508
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P72508
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CYC Query on CYC Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AB [auth T] SDF format, chain BA [auth C] SDF format, chain BB [auth T] SDF format, chain CA [auth D] SDF format, chain CB [auth U] SDF format, chain DA [auth D] SDF format, chain DB [auth V] SDF format, chain EA [auth E] SDF format, chain EB [auth V] SDF format, chain FA [auth F] SDF format, chain FB [auth W] SDF format, chain GA [auth F] SDF format, chain GB [auth X] SDF format, chain HA [auth G] SDF format, chain HB [auth X] SDF format, chain IA [auth H] SDF format, chain JA [auth H] SDF format, chain KA [auth I] SDF format, chain LA [auth J] SDF format, chain MA [auth J] SDF format, chain NA [auth K] SDF format, chain OA [auth L] SDF format, chain PA [auth L] SDF format, chain QA [auth M] SDF format, chain RA [auth N] SDF format, chain SA [auth N] SDF format, chain TA [auth O] SDF format, chain UA [auth P] SDF format, chain VA [auth P] SDF format, chain WA [auth Q] SDF format, chain XA [auth R] SDF format, chain Y [auth A] SDF format, chain YA [auth R] SDF format, chain Z [auth B] SDF format, chain ZA [auth S] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth T] MOL2 format, chain BA [auth C] MOL2 format, chain BB [auth T] MOL2 format, chain CA [auth D] MOL2 format, chain CB [auth U] MOL2 format, chain DA [auth D] MOL2 format, chain DB [auth V] MOL2 format, chain EA [auth E] MOL2 format, chain EB [auth V] MOL2 format, chain FA [auth F] MOL2 format, chain FB [auth W] MOL2 format, chain GA [auth F] MOL2 format, chain GB [auth X] MOL2 format, chain HA [auth G] MOL2 format, chain HB [auth X] MOL2 format, chain IA [auth H] MOL2 format, chain JA [auth H] MOL2 format, chain KA [auth I] MOL2 format, chain LA [auth J] MOL2 format, chain MA [auth J] MOL2 format, chain NA [auth K] MOL2 format, chain OA [auth L] MOL2 format, chain PA [auth L] MOL2 format, chain QA [auth M] MOL2 format, chain RA [auth N] MOL2 format, chain SA [auth N] MOL2 format, chain TA [auth O] MOL2 format, chain UA [auth P] MOL2 format, chain VA [auth P] MOL2 format, chain WA [auth Q] MOL2 format, chain XA [auth R] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth R] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth S] mmCIF format, chain AA [auth B] mmCIF format, chain AB [auth T] mmCIF format, chain BA [auth C] mmCIF format, chain BB [auth T] mmCIF format, chain CA [auth D] mmCIF format, chain CB [auth U] mmCIF format, chain DA [auth D] mmCIF format, chain DB [auth V] mmCIF format, chain EA [auth E] mmCIF format, chain EB [auth V] mmCIF format, chain FA [auth F] mmCIF format, chain FB [auth W] mmCIF format, chain GA [auth F] mmCIF format, chain GB [auth X] mmCIF format, chain HA [auth G] mmCIF format, chain HB [auth X] mmCIF format, chain IA [auth H] mmCIF format, chain JA [auth H] mmCIF format, chain KA [auth I] mmCIF format, chain LA [auth J] mmCIF format, chain MA [auth J] mmCIF format, chain NA [auth K] mmCIF format, chain OA [auth L] mmCIF format, chain PA [auth L] mmCIF format, chain QA [auth M] mmCIF format, chain RA [auth N] mmCIF format, chain SA [auth N] mmCIF format, chain TA [auth O] mmCIF format, chain UA [auth P] mmCIF format, chain VA [auth P] mmCIF format, chain WA [auth Q] mmCIF format, chain XA [auth R] mmCIF format, chain Y [auth A] mmCIF format, chain YA [auth R] mmCIF format, chain Z [auth B] mmCIF format, chain ZA [auth S]	AA [auth B] AB [auth T] BA [auth C] BB [auth T] CA [auth D] AA [auth B], AB [auth T], BA [auth C], BB [auth T], CA [auth D], CB [auth U], DA [auth D], DB [auth V], EA [auth E], EB [auth V], FA [auth F], FB [auth W], GA [auth F], GB [auth X], HA [auth G], HB [auth X], IA [auth H], JA [auth H], KA [auth I], LA [auth J], MA [auth J], NA [auth K], OA [auth L], PA [auth L], QA [auth M], RA [auth N], SA [auth N], TA [auth O], UA [auth P], VA [auth P], WA [auth Q], XA [auth R], Y [auth A], YA [auth R], Z [auth B], ZA [auth S]	PHYCOCYANOBILIN C₃₃ H₄₀ N₄ O₆ VXTXPYZGDQPMHK-GMXXPEQVSA-N		Interactions Focus chain AA [auth B] Focus chain AB [auth T] Focus chain BA [auth C] Focus chain BB [auth T] Focus chain CA [auth D] Focus chain CB [auth U] Focus chain DA [auth D] Focus chain DB [auth V] Focus chain EA [auth E] Focus chain EB [auth V] Focus chain FA [auth F] Focus chain FB [auth W] Focus chain GA [auth F] Focus chain GB [auth X] Focus chain HA [auth G] Focus chain HB [auth X] Focus chain IA [auth H] Focus chain JA [auth H] Focus chain KA [auth I] Focus chain LA [auth J] Focus chain MA [auth J] Focus chain NA [auth K] Focus chain OA [auth L] Focus chain PA [auth L] Focus chain QA [auth M] Focus chain RA [auth N] Focus chain SA [auth N] Focus chain TA [auth O] Focus chain UA [auth P] Focus chain VA [auth P] Focus chain WA [auth Q] Focus chain XA [auth R] Focus chain Y [auth A] Focus chain YA [auth R] Focus chain Z [auth B] Focus chain ZA [auth S] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth T] Focus chain BA [auth C] Focus chain BB [auth T] Focus chain CA [auth D] Focus chain CB [auth U] Focus chain DA [auth D] Focus chain DB [auth V] Focus chain EA [auth E] Focus chain EB [auth V] Focus chain FA [auth F] Focus chain FB [auth W] Focus chain GA [auth F] Focus chain GB [auth X] Focus chain HA [auth G] Focus chain HB [auth X] Focus chain IA [auth H] Focus chain JA [auth H] Focus chain KA [auth I] Focus chain LA [auth J] Focus chain MA [auth J] Focus chain NA [auth K] Focus chain OA [auth L] Focus chain PA [auth L] Focus chain QA [auth M] Focus chain RA [auth N] Focus chain SA [auth N] Focus chain TA [auth O] Focus chain UA [auth P] Focus chain VA [auth P] Focus chain WA [auth Q] Focus chain XA [auth R] Focus chain Y [auth A] Focus chain YA [auth R] Focus chain Z [auth B] Focus chain ZA [auth S]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MEN Query on MEN	B, D, F, H, J B, D, F, H, J, L, N, P, R, T, V, X	L-PEPTIDE LINKING	C₅ H₁₀ N₂ O₃		ASN

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.237
R-Value Work: 0.189
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109	α = 90
b = 117.5	β = 90.3
c = 185	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
X-PLOR	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2001-06-06

Deposition Author(s):

Liang, D.-C.

Chang, W.-R.

Wang, X.-Q.

Revision History (Full details and data files)

Version 1.0: 2001-06-06
Type: Initial release
Version 1.1: 2008-04-26
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2018-04-04
Changes: Advisory, Data collection
Version 1.4: 2023-12-27
Changes: Advisory, Data collection, Database references, Derived calculations