7DNR | pdb_00007dnr

Crystal Structure of Zn-bound SIS Domain of Glucosamine-6-P Synthase from E. coli

PDB DOI: https://doi.org/10.2210/pdb7DNR/pdb

Classification: ISOMERASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-12-10 Released: 2021-12-15
Deposition Author(s): Gao, C., Xiao, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.235 (Depositor), 0.228 (DCC)
R-Value Work:
0.214 (Depositor), 0.212 (DCC)
R-Value Observed:
0.215 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Discovery of Metal-binding Proteins by Thermal Proteome Profiling

Zeng, X., Wei, T., Liu, Y., Wang, X., Feng, T., Cheng, Y., Qin, W., Gao, C., Xiao, J., Wang, C.

To be published.

Macromolecule Content

Total Structure Weight: 80.91 kDa
Atom Count: 5,976
Modeled Residue Count: 711
Deposited Residue Count: 736
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamine--fructose-6-phosphate aminotransferase [isomerizing]	A, B	368	Escherichia coli K-12	Mutation(s): 0 Gene Names: glmS, b3729, JW3707 EC: 2.6.1.16
UniProt
Find proteins for P17169 (Escherichia coli (strain K12)) Explore P17169 Go to UniProtKB: P17169
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P17169
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.235 (Depositor), 0.228 (DCC)
R-Value Work: 0.214 (Depositor), 0.212 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.099	α = 90
b = 67.889	β = 111.44
c = 73.952	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2021-12-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-12-15
Type: Initial release
Version 1.1: 2023-11-29
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.