7YV0 | pdb_00007yv0

Structural Insight into a Metal-Dependent Mutase MtdL Revealing an Arginine Residue Covalently Mediated Interconversion between Nucleotide-Based furanose and pyranose

PDB DOI: https://doi.org/10.2210/pdb7YV0/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Marinactinospora thermotolerans
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2022-08-18 Released: 2023-07-26
Deposition Author(s): Chi, C.B., Ma, M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.34 Å
R-Value Free:
0.238 (Depositor), 0.241 (DCC)
R-Value Work:
0.201 (Depositor), 0.205 (DCC)
R-Value Observed:
0.203 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 7YV0

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

Literature

Structural Insight into a Metal-Dependent Mutase Revealing an Arginine Residue-Covalently Mediated Interconversion between Nucleotide-Based Pyranose and Furanose.

Chi, C.B., Xu, R., Chen, Q.Q., Zhang, X.H., Shi, X.M., Jin, H.W., Yin, F., Jia, H.L., Zhang, L.R., Yang, D.H., Ju, J.H., Li, Q.L., Ma, M.

(2023) ACS Catal 13: 1597-1603

DOI: https://doi.org/10.1021/acscatal.2c04907

Macromolecule Content

Total Structure Weight: 83.4 kDa
Atom Count: 5,931
Modeled Residue Count: 744
Deposited Residue Count: 752
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transglycosylse	A, B	376	Marinactinospora thermotolerans	Mutation(s): 0
UniProt
Find proteins for G8HX37 (Marinactinospora thermotolerans) Explore G8HX37 Go to UniProtKB: G8HX37
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G8HX37
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.34 Å
R-Value Free: 0.238 (Depositor), 0.241 (DCC)
R-Value Work: 0.201 (Depositor), 0.205 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 162.306	α = 90
b = 98.273	β = 97.98
c = 59.224	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-07-26

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-07-26
Type: Initial release
Version 1.1: 2024-10-16
Changes: Data collection, Structure summary

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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.