9CDR

DosP Apo straight form

PDB DOI: https://doi.org/10.2210/pdb9CDR/pdb
EM Map EMD-45485: EMDB EMDataResource

Classification: OXYGEN BINDING
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-06-25 Released: 2024-11-20
Deposition Author(s): Kumar, P., Kober, D.L.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.91 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structures of the multi-domain oxygen sensor DosP: remote control of a c-di-GMP phosphodiesterase by a regulatory PAS domain

Wu, W., Kumar, P., Brautigam, C.A., Tso, S.C., Baniasadi, H.R., Kober, D.L., Gilles-Gonzalez, M.A.

(2024) Nat Commun 15: 9653

DOI: https://doi.org/10.1038/s41467-024-53942-7

Macromolecule Content

Total Structure Weight: 183.61 kDa
Atom Count: 12,604
Modelled Residue Count: 1,574
Deposited Residue Count: 1,612
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxygen sensor protein DosP	A, B	806	Escherichia coli	Mutation(s): 0 Gene Names: dosP, dos, pdeO, yddU, b1489, JW1484 EC: 3.1.4.52
UniProt
Find proteins for P76129 (Escherichia coli (strain K12)) Explore P76129 Go to UniProtKB: P76129
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P76129
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) Query on HEM Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
OXY (Subject of Investigation/LOI) Query on OXY Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.91 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-11-20

Deposition Author(s):

Kumar, P.

Kober, D.L.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R00 GM141261
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U24 GM129547

Revision History (Full details and data files)

Version 1.0: 2024-11-20
Type: Initial release

Prepare Data

Validate Data

Deposit Data

Help and Resources

9CDR

DosP Apo straight form

Structures of the multi-domain oxygen sensor DosP: remote control of a c-di-GMP phosphodiesterase by a regulatory PAS domain

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)