7A73

Crystal structure of the two-domain cyclophilinA from Anabaena sp.

PDB DOI: https://doi.org/10.2210/pdb7A73/pdb

Classification: PLANT PROTEIN
Organism(s): Nostoc sp. PCC 7120 = FACHB-418
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-08-27 Released: 2021-10-06
Deposition Author(s): Yadav, S., Schleiff, E., Yildiz, O.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.14 Å
R-Value Free: 0.198
R-Value Work: 0.179
R-Value Observed: 0.180

wwPDB Validation 3D Report Full Report

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

Literature

The two-domain cyclophilin family protein anaCyp40 of Anabaena sp. regulates photosystem assembly and phycobilisome association

Yadav, S., Schleiff, E., Yildiz, O.

To be published.

Macromolecule Content

Total Structure Weight: 41.38 kDa
Atom Count: 3,198
Modelled Residue Count: 334
Deposited Residue Count: 375
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alr5059 protein	A	375	Nostoc sp. PCC 7120 = FACHB-418	Mutation(s): 0 Gene Names: alr5059
UniProt
Find proteins for Q8YM80 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)) Explore Q8YM80 Go to UniProtKB: Q8YM80
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8YM80
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.14 Å
R-Value Free: 0.198
R-Value Work: 0.179
R-Value Observed: 0.180
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.12	α = 90
b = 103.06	β = 114.74
c = 44.17	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
DIALS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-10-06

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	DFG SCHL585/7-2)

Revision History (Full details and data files)

Version 1.0: 2021-10-06
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.