8A8Y | pdb_00008a8y

Structure of truncated 1-deoxy-D-xylulose 5-phosphate synthase (DXS) from Klebsiella pneumoniae

PDB DOI: https://doi.org/10.2210/pdb8A8Y/pdb

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

Deposited: 2022-06-24 Released: 2023-07-05
Deposition Author(s): Adam, S., Hirsch, A.
Funding Organization(s): Helmholtz Association

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.201 (Depositor), 0.200 (DCC)
R-Value Work:
0.179 (Depositor), 0.180 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structure of truncated 1-deoxy-D-xylulose 5-phosphate synthase (DXS) from Klebsiella pneumoniae

Adam, S., Hirsch, A.

To be published.

Macromolecule Content

Total Structure Weight: 126.51 kDa
Atom Count: 7,776
Modeled Residue Count: 970
Deposited Residue Count: 1,172
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1-deoxy-D-xylulose-5-phosphate synthase	A, B	586	Klebsiella pneumoniae	Mutation(s): 0 Gene Names: dxs_3, dxs, dxs_1, dxs_2, BN49_1346, DRB11_07540, FXN67_12755, GPZ86_21160, NCTC11679_04435, NCTC13465_06397... dxs_3, dxs, dxs_1, dxs_2, BN49_1346, DRB11_07540, FXN67_12755, GPZ86_21160, NCTC11679_04435, NCTC13465_06397, NCTC3279_00555, NCTC5047_01280, NCTC5052_00313, NCTC9140_02292, NCTC9645_03343, NCTC9661_05006, SAMEA3512100_02923, SAMEA3649733_02709, SAMEA4364603_02966 EC: 2.2.1.7
UniProt
Find proteins for A6T5F3 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)) Explore A6T5F3 Go to UniProtKB: A6T5F3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A6T5F3
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.201 (Depositor), 0.200 (DCC)
R-Value Work: 0.179 (Depositor), 0.180 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.164	α = 90
b = 144.247	β = 90
c = 142.911	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-07-05

Deposition Author(s):

Funding Organization	Location	Grant Number
Helmholtz Association	Germany	--

Revision History (Full details and data files)

Version 1.0: 2023-07-05
Type: Initial release
Version 1.1: 2024-02-07
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.