8C7I | pdb_00008c7i

Crystal structure of the PS2 assembly factor Psb32 from the cyanobactium Thermosyncechococcus vestitus (formerly elongatus)

PDB DOI: https://doi.org/10.2210/pdb8C7I/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Aequorea victoria, Thermosynechococcus vestitus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2023-01-16 Released: 2024-01-31
Deposition Author(s): Liauw, P., Gasper, R., Nowaczyk, M.M., Hofmann, E.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free:
0.258 (Depositor), 0.258 (DCC)
R-Value Work:
0.227 (Depositor), 0.228 (DCC)
R-Value Observed:
0.229 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

Cryo-EM analysis of a novel photosystem II assembly intermediate that binds Psb32

Bohn, S., Lambertz, J., Lo, Y.K., Meier-Credo, J., Fuertges, T., Liauw, P., Gasper, R., Langer, J.D., Hofmann, E., Rudack, T., Schuller, J., Nowaczyk, M.M.

To be published.

Macromolecule Content

Total Structure Weight: 48.65 kDa
Atom Count: 3,197
Modeled Residue Count: 405
Deposited Residue Count: 437
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein,Tll0404 protein	A	437	Aequorea victoria, Thermosynechococcus vestitus This entity is chimeric	Mutation(s): 12 Gene Names: GFP, tll0404
UniProt
Find proteins for P42212 (Aequorea victoria) Explore P42212 Go to UniProtKB: P42212
Find proteins for Q8DLS4 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DLS4 Go to UniProtKB: Q8DLS4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	P42212 Q8DLS4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CRO Query on CRO	A	L-PEPTIDE LINKING	C₁₅ H₁₇ N₃ O₅		THR, TYR, GLY

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free: 0.258 (Depositor), 0.258 (DCC)
R-Value Work: 0.227 (Depositor), 0.228 (DCC)
R-Value Observed: 0.229 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.65	α = 90
b = 145.65	β = 90
c = 91.81	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
BALBES	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-01-31

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	GRK2341
German Research Foundation (DFG)	Germany	FOR2092
German Research Foundation (DFG)	Germany	SPP2002

Revision History (Full details and data files)

Version 1.0: 2024-01-31
Type: Initial release
Version 1.1: 2024-11-06
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.