8OFJ | pdb_00008ofj

Mycoplasma pneumoniae CdaM

PDB DOI: https://doi.org/10.2210/pdb8OFJ/pdb

Classification: TRANSFERASE
Organism(s): Mycoplasmoides pneumoniae 19294
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-03-15 Released: 2023-06-21
Deposition Author(s): Garbers, T.B., Neumann, P., Ficner, R.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.249 (Depositor), 0.250 (DCC)
R-Value Work:
0.198 (Depositor), 0.200 (DCC)

wwPDB Validation 3D Report Full Report

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

Literature

Streptococcus pneumoniae CdaA

Garbers, T.B., Neumann, P., Ficner, R.

To be published.

Macromolecule Content

Total Structure Weight: 36.8 kDa
Atom Count: 2,440
Modeled Residue Count: 304
Deposited Residue Count: 332
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diadenylate cyclase	A [auth B], B [auth A]	166	Mycoplasmoides pneumoniae 19294	Mutation(s): 0 Gene Names: dacB, MPN_244, K04_orf202, MP588 EC: 2.7.7.85
UniProt
Find proteins for P75528 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75528 Go to UniProtKB: P75528
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P75528
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.249 (Depositor), 0.250 (DCC)
R-Value Work: 0.198 (Depositor), 0.200 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.84	α = 90
b = 80.42	β = 93.13
c = 44.444	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-06-21

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	SPP 1879

Revision History (Full details and data files)

Version 1.0: 2023-06-21
Type: Initial release
Version 1.1: 2024-06-19
Changes: Data collection

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.