1PPR | pdb_00001ppr

PERIDININ-CHLOROPHYLL-PROTEIN OF AMPHIDINIUM CARTERAE

PDB DOI: https://doi.org/10.2210/pdb1PPR/pdb

Classification: LIGHT-HARVESTING PROTEIN
Organism(s): Amphidinium carterae
Mutation(s): No

Deposited: 1996-03-06 Released: 1997-08-20
Deposition Author(s): Hofmann, E., Welte, W., Diederichs, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.201 (Depositor), 0.188 (DCC)
R-Value Work:
0.179 (Depositor), 0.168 (DCC)
R-Value Observed:
0.179 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Structural basis of light harvesting by carotenoids: peridinin-chlorophyll-protein from Amphidinium carterae.

Hofmann, E., Wrench, P.M., Sharples, F.P., Hiller, R.G., Welte, W., Diederichs, K.

(1996) Science 272: 1788-1791

PubMed: 8650577 Search on PubMed
DOI: https://doi.org/10.1126/science.272.5269.1788
Primary Citation Related Structures:
1PPR

PubMed Abstract:
Peridinin-chlorophyll-protein, a water-soluble light-harvesting complex that has a blue-green absorbing carotenoid as its main pigment, is present in most photosynthetic dinoflagellates. Its high-resolution (2.0 angstrom) x-ray structure reveals a noncrystallographic trimer in which each polypeptide contains an unusual jellyroll fold of the alpha-helical amino- and carboxyl-terminal domains. These domains constitute a scaffold with pseudo-twofold symmetry surrounding a hydrophobic cavity filled by two lipid, eight peridinin, and two chlorophyll a molecules. The structural basis for efficient excitonic energy transfer from peridinin to chlorophyll is found in the clustering of peridinins around the chlorophylls at van der Waals distances.

Organizational Affiliation

Fakultät für Biologie, Universität Konstanz, Germany.

Macromolecule Content

Total Structure Weight: 123.8 kDa
Atom Count: 9,152
Modeled Residue Count: 936
Deposited Residue Count: 936
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PERIDININ-CHLOROPHYLL PROTEIN	A [auth M], B [auth N], C [auth O]	312	Amphidinium carterae	Mutation(s): 0
UniProt
Find proteins for P80484 (Amphidinium carterae) Explore P80484 Go to UniProtKB: P80484
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P80484
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DGD Query on DGD Download:Ideal Coordinates CCD File SDF format, chain AA [auth N] SDF format, chain BA [auth O] SDF format, chain MA [auth O] SDF format, chain N [auth M] SDF format, chain O [auth M] SDF format, chain Z [auth N] MOL2 format, chain AA [auth N] MOL2 format, chain BA [auth O] MOL2 format, chain MA [auth O] MOL2 format, chain N [auth M] MOL2 format, chain O [auth M] MOL2 format, chain Z [auth N] mmCIF format, chain AA [auth N] mmCIF format, chain BA [auth O] mmCIF format, chain MA [auth O] mmCIF format, chain N [auth M] mmCIF format, chain O [auth M] mmCIF format, chain Z [auth N]	AA [auth N] BA [auth O] MA [auth O] N [auth M] O [auth M] AA [auth N], BA [auth O], MA [auth O], N [auth M], O [auth M], Z [auth N]	DIGALACTOSYL DIACYL GLYCEROL (DGDG) C₅₁ H₉₆ O₁₅ LDQFLSUQYHBXSX-HXXRYREZSA-N		Interactions Focus chain AA [auth N] Focus chain BA [auth O] Focus chain MA [auth O] Focus chain N [auth M] Focus chain O [auth M] Focus chain Z [auth N] Interactions & Density Focus chain AA [auth N] Focus chain BA [auth O] Focus chain MA [auth O] Focus chain N [auth M] Focus chain O [auth M] Focus chain Z [auth N]
CLA Query on CLA Download:Ideal Coordinates CCD File SDF format, chain CA [auth O] SDF format, chain D [auth M] SDF format, chain DA [auth O] SDF format, chain E [auth M] SDF format, chain P [auth N] SDF format, chain Q [auth N] MOL2 format, chain CA [auth O] MOL2 format, chain D [auth M] MOL2 format, chain DA [auth O] MOL2 format, chain E [auth M] MOL2 format, chain P [auth N] MOL2 format, chain Q [auth N] mmCIF format, chain CA [auth O] mmCIF format, chain D [auth M] mmCIF format, chain DA [auth O] mmCIF format, chain E [auth M] mmCIF format, chain P [auth N] mmCIF format, chain Q [auth N]	CA [auth O] D [auth M] DA [auth O] E [auth M] P [auth N] CA [auth O], D [auth M], DA [auth O], E [auth M], P [auth N], Q [auth N]	CHLOROPHYLL A C₅₅ H₇₂ Mg N₄ O₅ ATNHDLDRLWWWCB-AENOIHSZSA-M		Interactions Focus chain CA [auth O] Focus chain D [auth M] Focus chain DA [auth O] Focus chain E [auth M] Focus chain P [auth N] Focus chain Q [auth N] Interactions & Density Focus chain CA [auth O] Focus chain D [auth M] Focus chain DA [auth O] Focus chain E [auth M] Focus chain P [auth N] Focus chain Q [auth N]
PID Query on PID Download:Ideal Coordinates CCD File SDF format, chain EA [auth O] SDF format, chain F [auth M] SDF format, chain FA [auth O] SDF format, chain G [auth M] SDF format, chain GA [auth O] SDF format, chain H [auth M] SDF format, chain HA [auth O] SDF format, chain I [auth M] SDF format, chain IA [auth O] SDF format, chain J [auth M] SDF format, chain JA [auth O] SDF format, chain KA [auth O] SDF format, chain L [auth M] SDF format, chain LA [auth O] SDF format, chain M SDF format, chain S [auth N] SDF format, chain T [auth N] SDF format, chain U [auth N] SDF format, chain V [auth N] SDF format, chain W [auth N] SDF format, chain X [auth N] SDF format, chain Y [auth N] SDF format, chain R [auth N] SDF format, chain K [auth M] MOL2 format, chain EA [auth O] MOL2 format, chain F [auth M] MOL2 format, chain FA [auth O] MOL2 format, chain G [auth M] MOL2 format, chain GA [auth O] MOL2 format, chain H [auth M] MOL2 format, chain HA [auth O] MOL2 format, chain I [auth M] MOL2 format, chain IA [auth O] MOL2 format, chain J [auth M] MOL2 format, chain JA [auth O] MOL2 format, chain KA [auth O] MOL2 format, chain L [auth M] MOL2 format, chain LA [auth O] MOL2 format, chain M MOL2 format, chain S [auth N] MOL2 format, chain T [auth N] MOL2 format, chain U [auth N] MOL2 format, chain V [auth N] MOL2 format, chain W [auth N] MOL2 format, chain X [auth N] MOL2 format, chain Y [auth N] MOL2 format, chain R [auth N] MOL2 format, chain K [auth M] mmCIF format, chain EA [auth O] mmCIF format, chain F [auth M] mmCIF format, chain FA [auth O] mmCIF format, chain G [auth M] mmCIF format, chain GA [auth O] mmCIF format, chain H [auth M] mmCIF format, chain HA [auth O] mmCIF format, chain I [auth M] mmCIF format, chain IA [auth O] mmCIF format, chain J [auth M] mmCIF format, chain JA [auth O] mmCIF format, chain KA [auth O] mmCIF format, chain L [auth M] mmCIF format, chain LA [auth O] mmCIF format, chain M mmCIF format, chain S [auth N] mmCIF format, chain T [auth N] mmCIF format, chain U [auth N] mmCIF format, chain V [auth N] mmCIF format, chain W [auth N] mmCIF format, chain X [auth N] mmCIF format, chain Y [auth N] mmCIF format, chain R [auth N] mmCIF format, chain K [auth M]	EA [auth O] F [auth M] FA [auth O] G [auth M] GA [auth O] EA [auth O], F [auth M], FA [auth O], G [auth M], GA [auth O], H [auth M], HA [auth O], I [auth M], IA [auth O], J [auth M], JA [auth O], K [auth M], KA [auth O], L [auth M], LA [auth O], M, R [auth N], S [auth N], T [auth N], U [auth N], V [auth N], W [auth N], X [auth N], Y [auth N]	PERIDININ C₃₉ H₅₀ O₇ UYRDHEJRPVSJFM-FROCQLDGSA-N		Interactions Focus chain EA [auth O] Focus chain F [auth M] Focus chain FA [auth O] Focus chain G [auth M] Focus chain GA [auth O] Focus chain H [auth M] Focus chain HA [auth O] Focus chain I [auth M] Focus chain IA [auth O] Focus chain J [auth M] Focus chain JA [auth O] Focus chain K [auth M] Focus chain KA [auth O] Focus chain L [auth M] Focus chain LA [auth O] Focus chain M Focus chain R [auth N] Focus chain S [auth N] Focus chain T [auth N] Focus chain U [auth N] Focus chain V [auth N] Focus chain W [auth N] Focus chain X [auth N] Focus chain Y [auth N] Interactions & Density Focus chain EA [auth O] Focus chain F [auth M] Focus chain FA [auth O] Focus chain G [auth M] Focus chain GA [auth O] Focus chain H [auth M] Focus chain HA [auth O] Focus chain I [auth M] Focus chain IA [auth O] Focus chain J [auth M] Focus chain JA [auth O] Focus chain K [auth M] Focus chain KA [auth O] Focus chain L [auth M] Focus chain LA [auth O] Focus chain M Focus chain R [auth N] Focus chain S [auth N] Focus chain T [auth N] Focus chain U [auth N] Focus chain V [auth N] Focus chain W [auth N] Focus chain X [auth N] Focus chain Y [auth N]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.201 (Depositor), 0.188 (DCC)
R-Value Work: 0.179 (Depositor), 0.168 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 198.426	α = 90
b = 116.296	β = 94.89
c = 67.025	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
XDS	data reduction
XSCALE	data scaling
X-PLOR	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 1997-08-20

Deposition Author(s):

Hofmann, E.

Welte, W.

Diederichs, K.

Revision History (Full details and data files)

Version 1.0: 1997-08-20
Type: Initial release
Version 1.1: 2008-03-03
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2011-08-17
Changes: Other
Version 2.0: 2024-02-14
Changes: Data collection, Database references, Derived calculations, Non-polymer description, Other