5TNV | pdb_00005tnv

Crystal Structure of a Xylose isomerase-like TIM barrel Protein from Mycobacterium smegmatis in Complex with Magnesium

PDB DOI: https://doi.org/10.2210/pdb5TNV/pdb

Classification: ISOMERASE
Organism(s): Mycolicibacterium smegmatis MC2 155
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-10-14 Released: 2016-11-09
Deposition Author(s): Cook, W.J., Fedorov, A.A., Fedorov, E.V., Huang, H., Bonanno, J.B., Gerlt, J.A., Almo, S.C.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.04 Å
R-Value Free:
0.137 (Depositor), 0.140 (DCC)
R-Value Work:
0.130 (DCC)
R-Value Observed:
0.116 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal Structure of a Xylose isomerase-like TIM barrel Protein from Mycobacterium smegmatis in Complex with Magnesium

Cook, W.J., Fedorov, A.A., Fedorov, E.V., Huang, H., Bonanno, J.B., Gerlt, J.A., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 36.27 kDa
Atom Count: 2,864
Modeled Residue Count: 306
Deposited Residue Count: 326
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AP endonuclease, family protein 2	A	326	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0 Gene Names: MSMEG_6790, MSMEI_6607
UniProt
Find proteins for A0R760 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R760 Go to UniProtKB: A0R760
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0R760
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-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: 1.04 Å
R-Value Free: 0.137 (Depositor), 0.140 (DCC)
R-Value Work: 0.130 (DCC)
R-Value Observed: 0.116 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.869	α = 90
b = 82.869	β = 90
c = 125.218	γ = 120

Software Package:

Software Name	Purpose
SHELXL	refinement
MOSFLM	data reduction
SCALA	data scaling
SHELXCD	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2016-11-09

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History (Full details and data files)

Version 1.0: 2016-11-09
Type: Initial release
Version 1.1: 2017-01-18
Changes: Database references, Structure summary
Version 1.2: 2017-05-03
Changes: Database references, Structure summary
Version 1.3: 2017-09-27
Changes: Author supporting evidence
Version 1.4: 2019-12-25
Changes: Author supporting evidence
Version 1.5: 2024-03-06
Changes: Data collection, Database references

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.