7TM4 | pdb_00007tm4

Crystal structure of apo 3-phosphoshikimate 1-carboxyvinyltransferase from Klebsiella pneumoniae

PDB DOI: https://doi.org/10.2210/pdb7TM4/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: 1.70 Å
R-Value Free:
0.213 (Depositor), 0.220 (DCC)
R-Value Work:
0.182 (Depositor), 0.190 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of apo 3-phosphoshikimate 1-carboxyvinyltransferase 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: 47.18 kDa
Atom Count: 3,284
Modeled Residue Count: 426
Deposited Residue Count: 435
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-phosphoshikimate 1-carboxyvinyltransferase	A	435	Klebsiella pneumoniae subsp. pneumoniae HS11286	Mutation(s): 0 Gene Names: aroA, KPHS_18160 EC: 2.5.1.19
UniProt
Find proteins for A0A0H3GV01 (Klebsiella pneumoniae subsp. pneumoniae (strain HS11286)) Explore A0A0H3GV01 Go to UniProtKB: A0A0H3GV01
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H3GV01
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NO3 Query on NO3 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.213 (Depositor), 0.220 (DCC)
R-Value Work: 0.182 (Depositor), 0.190 (DCC)
R-Value Observed: 0.203 (Depositor)

Diffraction Data: https://doi.org/10.18430/M37TM4

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.709	α = 90
b = 43.709	β = 90
c = 171.067	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

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.