7TM7

Crystal structure of Alpha-1,4 glucan phosphorylase from Klebsiella pneumoniae

PDB DOI: https://doi.org/10.2210/pdb7TM7/pdb

Classification: TRANSFERASE
Organism(s): Klebsiella pneumoniae subsp. pneumoniae HS11286
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-01-19 Released: 2022-02-02
Deposition Author(s): 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: 1.91 Å
R-Value Free: 0.213
R-Value Work: 0.171
R-Value Observed: 0.173

Starting Model: experimental
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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 Alpha-1,4 glucan phosphorylase from Klebsiella pneumoniae

Liu, L., Lovell, S., Battaile, K.P., Tillery, L., Shek, R., Craig, J.K., Barrett, L.K., Van Voorhis, W.C.

To be published.

Macromolecule Content

Total Structure Weight: 182.9 kDa
Atom Count: 13,565
Modelled Residue Count: 1,593
Deposited Residue Count: 1,608
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-1,4 glucan phosphorylase	A, B	804	Klebsiella pneumoniae subsp. pneumoniae HS11286	Mutation(s): 0 Gene Names: KPHS_49390 EC: 2.4.1.1
UniProt
Find proteins for A0A0H3GYH4 (Klebsiella pneumoniae subsp. pneumoniae (strain HS11286)) Explore A0A0H3GYH4 Go to UniProtKB: A0A0H3GYH4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H3GYH4
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: 1.91 Å
R-Value Free: 0.213
R-Value Work: 0.171
R-Value Observed: 0.173
Space Group: P 2₁ 2₁ 2₁
Diffraction Data: https://doi.org/10.18430/M37TM7

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.862	α = 90
b = 150.386	β = 90
c = 156.352	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-02-02

Deposition Author(s):

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: 2022-02-02
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Refinement description

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.