7B6G | pdb_00007b6g

Crystal structure of MurE from E.coli in complex with Z1675346324

PDB DOI: https://doi.org/10.2210/pdb7B6G/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-12-07 Released: 2021-01-13
Deposition Author(s): Koekemoer, L., Steindel, M., Fairhead, M., Talon, R., Douangamath, A., Arrowsmith, C.H., Edwards, A.M., Bountra, C., von Delft, F., Krojer, T., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free:
0.256 (Depositor), 0.259 (DCC)
R-Value Work:
0.205 (Depositor), 0.211 (DCC)

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 MurE from E.coli

Koekemoer, L., Steindel, M., Fairhead, M., Talon, R., Douangamath, A., Arrowsmith, C.H., Edwards, A.M., Bountra, C., von Delft, F., Krojer, T.

To be published.

Macromolecule Content

Total Structure Weight: 107.35 kDa
Atom Count: 7,649
Modeled Residue Count: 960
Deposited Residue Count: 992
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase	A [auth AAA], B [auth BBB]	496	Escherichia coli	Mutation(s): 0 Gene Names: murE, GHR40_01000, NCTC12650_04426 EC: 6.3.2.13

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NUJ (Subject of Investigation/LOI) Query on NUJ Download:Ideal Coordinates CCD File SDF format, chain D [auth BBB] MOL2 format, chain D [auth BBB] mmCIF format, chain D [auth BBB]	D [auth BBB]	trans-3-[(2,6-dimethylpyrimidin-4-yl)(methyl)amino]cyclobutan-1-ol C₁₁ H₁₇ N₃ O SEZOHQAJJCEOMQ-MGCOHNPYSA-N		Interactions Focus chain D [auth BBB] Interactions & Density Focus chain D [auth BBB]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain C [auth AAA] SDF format, chain E [auth BBB] MOL2 format, chain C [auth AAA] MOL2 format, chain E [auth BBB] mmCIF format, chain C [auth AAA] mmCIF format, chain E [auth BBB]	C [auth AAA], E [auth BBB]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain C [auth AAA] Focus chain E [auth BBB] Interactions & Density Focus chain C [auth AAA] Focus chain E [auth BBB]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.256 (Depositor), 0.259 (DCC)
R-Value Work: 0.205 (Depositor), 0.211 (DCC)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.276	α = 97.234
b = 58.293	β = 91.447
c = 74.115	γ = 105.313

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2021-01-13

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2021-01-13
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Database references, Derived calculations, Refinement description