7T7J

Crystal Structure of Phosphoserine aminotransferase from Klebsiella pneumoniae subsp. pneumoniae in complex with Pyridoxal phosphate

PDB DOI: https://doi.org/10.2210/pdb7T7J/pdb

Classification: TRANSFERASE
Organism(s): Klebsiella pneumoniae subsp. pneumoniae HS11286
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2021-12-15 Released: 2022-01-12
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: 1.50 Å
R-Value Free: 0.160
R-Value Work: 0.128
R-Value Observed: 0.129

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of Phosphoserine aminotransferase from Klebsiella pneumoniae subsp. pneumoniae in complex with Pyridoxal phosphate

Abendroth, J., Davies, D.R., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 81.98 kDa
Atom Count: 6,804
Modelled Residue Count: 717
Deposited Residue Count: 740
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoserine aminotransferase	A, B	370	Klebsiella pneumoniae subsp. pneumoniae HS11286	Mutation(s): 1 Gene Names: serC, KPHS_18150 EC: 2.6.1.52
UniProt
Find proteins for A6T700 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)) Explore A6T700 Go to UniProtKB: A6T700
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A6T700
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP (Subject of Investigation/LOI) Query on PLP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.160
R-Value Work: 0.128
R-Value Observed: 0.129
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/M37T7J

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.21	α = 90
b = 80.66	β = 104.065
c = 86.82	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-01-12

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: 2022-01-12
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection

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.