6VR7 | pdb_00006vr7

Structure of a pseudomurein peptide ligase type C from Methanothermus fervidus

PDB DOI: https://doi.org/10.2210/pdb6VR7/pdb

Classification: LIGASE
Organism(s): Methanothermus fervidus
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2020-02-06 Released: 2021-02-10
Deposition Author(s): Carbone, V., Schofield, L.R., Sutherland-Smith, A.J., Ronimus, R.S., Subedi, B.P.
Funding Organization(s): Royal Society of New Zealand

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.279 (Depositor), 0.280 (DCC)
R-Value Work:
0.213 (Depositor), 0.219 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Archaeal pseudomurein and bacterial murein cell wall biosynthesis share a common evolutionary ancestry

Subedi, B.P., Martin, W.F., Carbone, V., Duin, E.C., Cronin, B., Sauter, J., Schofield, L.R., Sutherland-Smith, A.J., Ronimus, R.S.

(2021) FEMS Microbes 2

DOI: https://doi.org/10.1093/femsmc/xtab012

Macromolecule Content

Total Structure Weight: 55.01 kDa
Atom Count: 3,839
Modeled Residue Count: 485
Deposited Residue Count: 492
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mur ligase middle domain protein	A	492	Methanothermus fervidus	Mutation(s): 0 Gene Names: Mfer_0336
UniProt
Find proteins for E3GXV7 (Methanothermus fervidus (strain ATCC 43054 / DSM 2088 / JCM 10308 / V24 S)) Explore E3GXV7 Go to UniProtKB: E3GXV7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E3GXV7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AAE (Subject of Investigation/LOI) Query on AAE Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	ACETOACETIC ACID C₄ H₆ O₃ WDJHALXBUFZDSR-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.279 (Depositor), 0.280 (DCC)
R-Value Work: 0.213 (Depositor), 0.219 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.802	α = 90
b = 97.802	β = 90
c = 138.351	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
MoRDa	phasing
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-02-10

Deposition Author(s):

Carbone, V.

Schofield, L.R.

Sutherland-Smith, A.J.

Ronimus, R.S.

Subedi, B.P.

Funding Organization	Location	Grant Number
Royal Society of New Zealand	New Zealand	AGR1301

Revision History (Full details and data files)

Version 1.0: 2021-02-10
Type: Initial release
Version 2.0: 2021-07-28
Type: Coordinate replacement
Reason: Ligand geometry
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary
Version 2.1: 2021-09-29
Changes: Database references
Version 2.2: 2023-10-11
Changes: Data collection, Database references, Refinement description