7FJ8 | pdb_00007fj8

KpAckA (PduW) with AMP complex structure

PDB DOI: https://doi.org/10.2210/pdb7FJ8/pdb

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

Deposited: 2021-08-03 Released: 2022-08-10
Deposition Author(s): Wu, W., Zhang, Q., Bartlam, M.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.215 (Depositor), 0.210 (DCC)
R-Value Work:
0.177 (Depositor), 0.180 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

KpAckA (PduW) with AMP complex structure

Wu, W., Zhang, Q., Bartlam, M.

To be published.

Macromolecule Content

Total Structure Weight: 87.68 kDa
Atom Count: 5,909
Modeled Residue Count: 737
Deposited Residue Count: 808
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable propionate kinase	A, B	404	Klebsiella pneumoniae	Mutation(s): 0 EC: 2.7.2.15
UniProt
Find proteins for A6TDE9 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)) Explore A6TDE9 Go to UniProtKB: A6TDE9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A6TDE9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP (Subject of Investigation/LOI) Query on AMP Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.215 (Depositor), 0.210 (DCC)
R-Value Work: 0.177 (Depositor), 0.180 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.098	α = 90
b = 152.635	β = 90
c = 131.743	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-08-10

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31800627
National Natural Science Foundation of China (NSFC)	China	31870053

Revision History (Full details and data files)

Version 1.0: 2022-08-10
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description
Version 1.2: 2024-11-20
Changes: Structure summary

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.