8K3H | pdb_00008k3h

Cryo-EM structure of PseP with NAD at 2.86 angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb8K3H/pdb
EM Map EMD-36851: EMDB EMDataResource

Classification: LYASE
Organism(s): Pseudomonas fluorescens
Expression System: Streptomyces lividans TK24
Mutation(s): No

Deposited: 2023-07-15 Released: 2024-07-17
Deposition Author(s): Mori, T., Awakawa, T., Adachi, N., Abe, I.
Funding Organization(s): Japan Agency for Medical Research and Development (AMED)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.86 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8K3H

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

Literature

Cryo-EM structure of PseP with NAD at 2.86 angstrom resolution

Mori, T., Awakawa, T., Adachi, N., Abe, I.

To be published.

Macromolecule Content

Total Structure Weight: 183.23 kDa
Atom Count: 7,460
Modeled Residue Count: 960
Deposited Residue Count: 1,630
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PseP	A, B	815	Pseudomonas fluorescens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	A, B	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.86 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION	3.1.3

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-07-17

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP21am0101071
Japan Agency for Medical Research and Development (AMED)	Japan	JP22ama121001

Revision History (Full details and data files)

Version 1.0: 2024-07-17
Type: Initial release
Version 1.1: 2025-07-02
Changes: Data collection, Structure summary

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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.