5UI2

CRYSTAL STRUCTURE OF ORANGE CAROTENOID PROTEIN

PDB DOI: https://doi.org/10.2210/pdb5UI2/pdb
Entry: 5UI2 supersedes: 1M98

Classification: carotenoid binding protein
Organism(s): Limnospira maxima
Mutation(s): No

Deposited: 2017-01-12 Released: 2017-01-25
Deposition Author(s): KERFELD, C.A., SAWAYA, M.R., VISHNU, B., KROGMANN, D., YEATES, T.O.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), United States Department of Agriculture (USDA)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.266
R-Value Work: 0.213
R-Value Observed: 0.215

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

The crystal structure of a cyanobacterial water-soluble carotenoid binding protein.

Kerfeld, C.A., Sawaya, M.R., Brahmandam, V., Cascio, D., Ho, K.K., Trevithick-Sutton, C.C., Krogmann, D.W., Yeates, T.O.

(2003) Structure 11: 55-65

PubMed: 12517340 Search on PubMed
DOI: https://doi.org/10.1016/s0969-2126(02)00936-x
Primary Citation of Related Structures:
5UI2

PubMed Abstract:
Carotenoids undergo a wide range of photochemical reactions in animal, plant, and microbial systems. In photosynthetic organisms, in addition to light harvesting, they perform an essential role in protecting against light-induced damage by quenching singlet oxygen, superoxide anion radicals, or triplet-state chlorophyll. We have determined the crystal structure of a water-soluble orange carotenoid protein (OCP) isolated from the cyanobacterium Arthrospira maxima at a resolution of 2.1 A. OCP forms a homodimer with one carotenoid molecule per monomer. The carotenoid binding site is lined by a striking number of methionine residues. The structure reveals several possible ways in which the protein environment influences the spectral properties of the pigment and provides insight into how the OCP carries out its putative functions in photoprotection.

Organizational Affiliation

Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA. kerfeld@mbi.ucla.edu

Macromolecule Content

Total Structure Weight: 72.29 kDa
Atom Count: 5,367
Modelled Residue Count: 630
Deposited Residue Count: 634
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orange carotenoid-binding protein	A, B	317	Limnospira maxima	Mutation(s): 0
UniProt
Find proteins for P83689 (Limnospira maxima) Explore P83689 Go to UniProtKB: P83689
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P83689
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	C	2		N/A	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EQ3 Query on EQ3 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B]	E [auth A], G [auth B]	(3'R)-3'-hydroxy-beta,beta-caroten-4-one C₄₀ H₅₄ O₂ ZRCXVNZZDQGBQT-BANQPSJHSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B]	D [auth A], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003 Query on PRD_900003	C	sucrose	Oligosaccharide / Nutrient		Interactions Focus chain C Interactions & Density Focus chain C

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.266
R-Value Work: 0.213
R-Value Observed: 0.215
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 217.2	α = 90
b = 40.761	β = 95.8
c = 75.46	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-01-25

Deposition Author(s):

This entry supersedes: 1M98

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	NIH GM 31299
United States Department of Agriculture (USDA)	United States	USDA1999-01759

Revision History (Full details and data files)

Version 1.0: 2017-01-25
Type: Initial release
Version 1.1: 2017-09-27
Changes: Author supporting evidence
Version 1.2: 2018-10-10
Changes: Data collection, Database references, Structure summary
Version 1.3: 2020-01-01
Changes: Author supporting evidence, Structure summary
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2024-03-06
Changes: Data collection, Database references, Structure summary