5DXD | pdb_00005dxd

Crystal structure of Putative beta-glucanase (Rv0315 ortholog) from Mycobacterium abscessus

PDB DOI: https://doi.org/10.2210/pdb5DXD/pdb

Classification: HYDROLASE
Organism(s): Mycobacteroides abscessus ATCC 19977
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-09-23 Released: 2015-11-04
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.189 (Depositor), 0.190 (DCC)
R-Value Work:
0.149 (Depositor), 0.149 (DCC)
R-Value Observed:
0.153 (Depositor)

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

Literature

Crystal structure of Putative beta-glucanase (Rv0315 ortholog) from Mycobacterium abcesus

Abendroth, J., Davies, D.R., Lorimer, D.D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 58.21 kDa
Atom Count: 4,129
Modeled Residue Count: 466
Deposited Residue Count: 514
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative beta-glucanase	A, B	257	Mycobacteroides abscessus ATCC 19977	Mutation(s): 0 Gene Names: MAB_1840c
UniProt
Find proteins for B1MNM2 (Mycobacteroides abscessus (strain ATCC 19977 / DSM 44196 / CCUG 20993 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543 / L948)) Explore B1MNM2 Go to UniProtKB: B1MNM2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B1MNM2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.189 (Depositor), 0.190 (DCC)
R-Value Work: 0.149 (Depositor), 0.149 (DCC)
R-Value Observed: 0.153 (Depositor)

Diffraction Data:

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.39	α = 90
b = 52.39	β = 90
c = 223.35	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
ARP	model building
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-11-04

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2015-11-04
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, 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.