7QRL

LytM domain of DipM, a coordinator of a complex net of autolysins in Caulobacter crescentus

PDB DOI: https://doi.org/10.2210/pdb7QRL/pdb

Classification: CELL CYCLE
Organism(s): Caulobacter vibrioides
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-01-11 Released: 2023-06-21
Deposition Author(s): Batuecas, M.T., Miguel-Ruano, V., Hermoso, J.A.
Funding Organization(s): Spanish Ministry of Science, Innovation, and Universities

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.219
R-Value Work: 0.188
R-Value Observed: 0.189

wwPDB Validation 3D Report Full Report

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

Literature

LytM domain of DipM, a coordinator of a complex net of autolysins in Caulobacter crescentus

Batuecas, M.T., Miguel-Ruano, V., Hermoso, J.A.

(2023) Nat Commun

Macromolecule Content

Total Structure Weight: 61.75 kDa
Atom Count: 4,902
Modelled Residue Count: 584
Deposited Residue Count: 584
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DipM	A, B	143	Caulobacter vibrioides	Mutation(s): 0 Gene Names: dipM, CC_1996
UniProt
Find proteins for A0A0H3C9Q9 (Caulobacter vibrioides (strain NA1000 / CB15N)) Explore A0A0H3C9Q9 Go to UniProtKB: A0A0H3C9Q9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H3C9Q9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DipM	C, D	149	Caulobacter vibrioides	Mutation(s): 0 Gene Names: dipM, CC_1996
UniProt
Find proteins for A0A0H3C9Q9 (Caulobacter vibrioides (strain NA1000 / CB15N)) Explore A0A0H3C9Q9 Go to UniProtKB: A0A0H3C9Q9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H3C9Q9
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.219
R-Value Work: 0.188
R-Value Observed: 0.189
Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.869	α = 90
b = 105.839	β = 90
c = 108.431	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-06-21

Deposition Author(s):

Miguel-Ruano, V.

Funding Organization	Location	Grant Number
Spanish Ministry of Science, Innovation, and Universities	Spain	BFU2017-90030-P

Revision History (Full details and data files)

Version 1.0: 2023-06-21
Type: Initial release
Version 1.1: 2024-02-07
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.