7UG3 | pdb_00007ug3

Crystal structure of adenosylmethionie-8-amino-7-oxononanoate aminotransferase from Klebsiella pneumoniae

PDB DOI: https://doi.org/10.2210/pdb7UG3/pdb

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

Deposited: 2022-03-23 Released: 2022-07-20
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.260 (Depositor), 0.211 (DCC)
R-Value Work:
0.225 (Depositor), 0.195 (DCC)
R-Value Observed:
0.225 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7UG3

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

Literature

Crystal structure of adenosylmethionie-8-amino-7-oxononanoate aminotransferase from Klebsiella pneumoniae

Yang, M., Edwards, T.E., Horanyi, P.S., Lorimer, D.D.

To be published.

Macromolecule Content

Total Structure Weight: 193.36 kDa
Atom Count: 12,851
Modeled Residue Count: 1,556
Deposited Residue Count: 1,752
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosylmethionine-8-amino-7-oxononanoate aminotransferase	A, B, C, D	438	Klebsiella pneumoniae	Mutation(s): 0 Gene Names: bioA, B4U61_18450, B5L96_06770, SAMEA4873619_00999 EC: 2.6.1.62
UniProt
Find proteins for A0A422Z2E3 (Klebsiella pneumoniae) Explore A0A422Z2E3 Go to UniProtKB: A0A422Z2E3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A422Z2E3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain G [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth D] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth D] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth C], H [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.260 (Depositor), 0.211 (DCC)
R-Value Work: 0.225 (Depositor), 0.195 (DCC)
R-Value Observed: 0.225 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.07	α = 90
b = 90.83	β = 93.874
c = 103.86	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
MoRDa	phasing
PDB_EXTRACT	data extraction
Coot	model building

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-07-20

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700059C

Revision History (Full details and data files)

Version 1.0: 2022-07-20
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Refinement description

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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.