5B13 | pdb_00005b13

Crystal structure of phycoerythrin

PDB DOI: https://doi.org/10.2210/pdb5B13/pdb

Classification: PHOTOSYNTHESIS
Organism(s): Palmaria palmata
Mutation(s): No

Deposited: 2015-11-18 Released: 2016-10-05
Deposition Author(s): Tanaka, Y., Gai, Z., Kishimura, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free:
0.236 (Depositor), 0.237 (DCC)
R-Value Work:
0.198 (Depositor), 0.200 (DCC)
R-Value Observed:
0.200 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structural properties of phycoerythrin from dulse palmaria palmata

Miyabe, Y., Furuta, T., Takeda, T., Kanno, G., Shimizu, T., Tanaka, Y., Gai, Z., Yasui, H., Kishimura, H.

(2016) J Food Biochem

Macromolecule Content

Total Structure Weight: 234.17 kDa
Atom Count: 18,212
Modeled Residue Count: 2,046
Deposited Residue Count: 2,046
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phycoerythrin alpha subunit	A C [auth B] D [auth C] E [auth D] F [auth E] A, C [auth B], D [auth C], E [auth D], F [auth E], G [auth F]	164	Palmaria palmata	Mutation(s): 0
UniProt
Find proteins for F2ZAL8 (Palmaria palmata) Explore F2ZAL8 Go to UniProtKB: F2ZAL8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F2ZAL8
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Phycoerythrin beta subunit	B [auth G] H I J K B [auth G], H, I, J, K, L	177	Palmaria palmata	Mutation(s): 0
UniProt
Find proteins for F2ZAL7 (Palmaria palmata) Explore F2ZAL7 Go to UniProtKB: F2ZAL7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F2ZAL7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PUB Query on PUB Download:Ideal Coordinates CCD File SDF format, chain DA [auth H] SDF format, chain GA [auth I] SDF format, chain JA [auth J] SDF format, chain MA [auth K] SDF format, chain Q [auth G] SDF format, chain PA [auth L] MOL2 format, chain DA [auth H] MOL2 format, chain GA [auth I] MOL2 format, chain JA [auth J] MOL2 format, chain MA [auth K] MOL2 format, chain Q [auth G] MOL2 format, chain PA [auth L] mmCIF format, chain DA [auth H] mmCIF format, chain GA [auth I] mmCIF format, chain JA [auth J] mmCIF format, chain MA [auth K] mmCIF format, chain Q [auth G] mmCIF format, chain PA [auth L]	DA [auth H] GA [auth I] JA [auth J] MA [auth K] PA [auth L] DA [auth H], GA [auth I], JA [auth J], MA [auth K], PA [auth L], Q [auth G]	PHYCOUROBILIN C₃₃ H₄₂ N₄ O₆ KDCCOOGTVSRCHX-YYVBKQGDSA-N		Interactions Focus chain DA [auth H] Focus chain GA [auth I] Focus chain JA [auth J] Focus chain MA [auth K] Focus chain PA [auth L] Focus chain Q [auth G] Interactions & Density Focus chain DA [auth H] Focus chain GA [auth I] Focus chain JA [auth J] Focus chain MA [auth K] Focus chain PA [auth L] Focus chain Q [auth G]
CYC Query on CYC Download:Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain BA [auth H] SDF format, chain CA [auth H] SDF format, chain EA [auth I] SDF format, chain FA [auth I] SDF format, chain HA [auth J] SDF format, chain IA [auth J] SDF format, chain KA [auth K] SDF format, chain LA [auth K] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth L] SDF format, chain O [auth G] SDF format, chain OA [auth L] SDF format, chain P [auth G] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain X [auth E] SDF format, chain Y [auth E] SDF format, chain Z [auth F] MOL2 format, chain AA [auth F] MOL2 format, chain BA [auth H] MOL2 format, chain CA [auth H] MOL2 format, chain EA [auth I] MOL2 format, chain FA [auth I] MOL2 format, chain HA [auth J] MOL2 format, chain IA [auth J] MOL2 format, chain KA [auth K] MOL2 format, chain LA [auth K] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth L] MOL2 format, chain O [auth G] MOL2 format, chain OA [auth L] MOL2 format, chain P [auth G] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain X [auth E] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth F] mmCIF format, chain AA [auth F] mmCIF format, chain BA [auth H] mmCIF format, chain CA [auth H] mmCIF format, chain EA [auth I] mmCIF format, chain FA [auth I] mmCIF format, chain HA [auth J] mmCIF format, chain IA [auth J] mmCIF format, chain KA [auth K] mmCIF format, chain LA [auth K] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth L] mmCIF format, chain O [auth G] mmCIF format, chain OA [auth L] mmCIF format, chain P [auth G] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain V [auth D] mmCIF format, chain W [auth D] mmCIF format, chain X [auth E] mmCIF format, chain Y [auth E] mmCIF format, chain Z [auth F]	AA [auth F] BA [auth H] CA [auth H] EA [auth I] FA [auth I] AA [auth F], BA [auth H], CA [auth H], EA [auth I], FA [auth I], HA [auth J], IA [auth J], KA [auth K], LA [auth K], M [auth A], N [auth A], NA [auth L], O [auth G], OA [auth L], P [auth G], R [auth B], S [auth B], T [auth C], U [auth C], V [auth D], W [auth D], X [auth E], Y [auth E], Z [auth F]	PHYCOCYANOBILIN C₃₃ H₄₀ N₄ O₆ VXTXPYZGDQPMHK-GMXXPEQVSA-N		Interactions Focus chain AA [auth F] Focus chain BA [auth H] Focus chain CA [auth H] Focus chain EA [auth I] Focus chain FA [auth I] Focus chain HA [auth J] Focus chain IA [auth J] Focus chain KA [auth K] Focus chain LA [auth K] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth L] Focus chain O [auth G] Focus chain OA [auth L] Focus chain P [auth G] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth E] Focus chain Y [auth E] Focus chain Z [auth F] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth H] Focus chain CA [auth H] Focus chain EA [auth I] Focus chain FA [auth I] Focus chain HA [auth J] Focus chain IA [auth J] Focus chain KA [auth K] Focus chain LA [auth K] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth L] Focus chain O [auth G] Focus chain OA [auth L] Focus chain P [auth G] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth E] Focus chain Y [auth E] Focus chain Z [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free: 0.236 (Depositor), 0.237 (DCC)
R-Value Work: 0.198 (Depositor), 0.200 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 187.5	α = 90
b = 111.85	β = 91.88
c = 112.67	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-10-05

Deposition Author(s):

Tanaka, Y.

Gai, Z.

Kishimura, H.

Revision History (Full details and data files)

Version 1.0: 2016-10-05
Type: Initial release
Version 1.1: 2016-10-12
Changes: Database references
Version 1.2: 2020-02-26
Changes: Advisory, Data collection, Database references, Derived calculations
Version 1.3: 2024-11-13
Changes: Data collection, Database references, Structure summary