7SSF | pdb_00007ssf

Light harvesting phycobiliprotein HaPE560 from the cryptophyte Hemiselmis andersenii CCMP644

PDB DOI: https://doi.org/10.2210/pdb7SSF/pdb

Classification: PHOTOSYNTHESIS
Organism(s): Hemiselmis andersenii
Mutation(s): No

Deposited: 2021-11-10 Released: 2023-10-25
Deposition Author(s): Rathbone, H.W., Michie, K.A., Laos, A.L., Curmi, P.M.G.
Funding Organization(s): Australian Research Council (ARC), Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.192 (Depositor), 0.190 (DCC)
R-Value Work:
0.154 (Depositor), 0.150 (DCC)
R-Value Observed:
0.156 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Molecular dissection of the soluble photosynthetic antenna from the cryptophyte alga Hemiselmis andersenii

Rathbone, H.W., Curmi, P.M.G., Michie, K.A., Green, B.R., Laos, A.L., Thordarson, P., Iranmanesh, H.

(2023) Commun Biol

DOI: https://doi.org/10.1038/s42003-023-05508-4

Macromolecule Content

Total Structure Weight: 114.3 kDa
Atom Count: 9,395
Modelled Residue Count: 985
Deposited Residue Count: 996
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HaPE560 alpha subunit	A, C, E, G	72	Hemiselmis andersenii	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Phycoerythrin550 beta subunit	B, D, F, H	177	Hemiselmis andersenii	Mutation(s): 0
UniProt
Find proteins for U5T8W0 (Hemiselmis andersenii) Explore U5T8W0 Go to UniProtKB: U5T8W0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	U5T8W0
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AX9 (Subject of Investigation/LOI) Query on AX9 Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain O [auth D] SDF format, chain S [auth F] SDF format, chain Y [auth H] MOL2 format, chain J [auth B] MOL2 format, chain O [auth D] MOL2 format, chain S [auth F] MOL2 format, chain Y [auth H] mmCIF format, chain J [auth B] mmCIF format, chain O [auth D] mmCIF format, chain S [auth F] mmCIF format, chain Y [auth H]	J [auth B], O [auth D], S [auth F], Y [auth H]	DiCys-(15,16)-Dihydrobiliverdin C₃₃ H₄₀ N₄ O₆ MZFCOERRVCGRTL-ZTYGKHTCSA-N		Interactions Focus chain J [auth B] Focus chain O [auth D] Focus chain S [auth F] Focus chain Y [auth H] Interactions & Density Focus chain J [auth B] Focus chain O [auth D] Focus chain S [auth F] Focus chain Y [auth H]
PEB (Subject of Investigation/LOI) Query on PEB Download Ideal Coordinates CCD File SDF format, chain AA [auth H] SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain P [auth D] SDF format, chain Q [auth D] SDF format, chain R [auth E] SDF format, chain T [auth F] SDF format, chain U [auth F] SDF format, chain X [auth G] SDF format, chain Z [auth H] SDF format, chain N [auth C] MOL2 format, chain AA [auth H] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth E] MOL2 format, chain T [auth F] MOL2 format, chain U [auth F] MOL2 format, chain X [auth G] MOL2 format, chain Z [auth H] MOL2 format, chain N [auth C] mmCIF format, chain AA [auth H] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth E] mmCIF format, chain T [auth F] mmCIF format, chain U [auth F] mmCIF format, chain X [auth G] mmCIF format, chain Z [auth H] mmCIF format, chain N [auth C]	AA [auth H] I [auth A] K [auth B] L [auth B] N [auth C] AA [auth H], I [auth A], K [auth B], L [auth B], N [auth C], P [auth D], Q [auth D], R [auth E], T [auth F], U [auth F], X [auth G], Z [auth H]	PHYCOERYTHROBILIN C₃₃ H₄₀ N₄ O₆ NKCBCVIFPXGHAV-WAVSMFBNSA-N		Interactions Focus chain AA [auth H] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain U [auth F] Focus chain X [auth G] Focus chain Z [auth H] Interactions & Density Focus chain AA [auth H] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain U [auth F] Focus chain X [auth G] Focus chain Z [auth H]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain BA [auth H] SDF format, chain M [auth B] SDF format, chain V [auth F] MOL2 format, chain BA [auth H] MOL2 format, chain M [auth B] MOL2 format, chain V [auth F] mmCIF format, chain BA [auth H] mmCIF format, chain M [auth B] mmCIF format, chain V [auth F]	BA [auth H], M [auth B], V [auth F]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain BA [auth H] Focus chain M [auth B] Focus chain V [auth F] Interactions & Density Focus chain BA [auth H] Focus chain M [auth B] Focus chain V [auth F]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain W [auth F] MOL2 format, chain W [auth F] mmCIF format, chain W [auth F]	W [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain W [auth F] Interactions & Density Focus chain W [auth F]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LYZ Query on LYZ	A, C, E, G	L-PEPTIDE LINKING	C₆ H₁₄ N₂ O₃		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.192 (Depositor), 0.190 (DCC)
R-Value Work: 0.154 (Depositor), 0.150 (DCC)
R-Value Observed: 0.156 (Depositor)

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.32	α = 90
b = 67.97	β = 99.33
c = 184.494	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
pointless	data scaling
Aimless	data scaling
PHENIX	phasing
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-10-25

Deposition Author(s):

Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	DP180103964
Other government	Australia	FA2386-17-1-4101 (U.S. Air Force Office of Scientific Research through the Asian Office of Aerospace Research and Developmen)
Australian Research Council (ARC)	Australia	LE190100165