7QRL | pdb_00007qrl

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 (Depositor), 0.230 (DCC)
R-Value Work:
0.188 (Depositor), 0.190 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
View more details

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
Modeled 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 (Depositor), 0.230 (DCC)
R-Value Work: 0.188 (Depositor), 0.190 (DCC)
R-Value Observed: 0.189 (Depositor)

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 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.