7LV6 | pdb_00007lv6

The structure of MalL mutant enzyme S536R from Bacillus subtilis

PDB DOI: https://doi.org/10.2210/pdb7LV6/pdb

Classification: HYDROLASE
Organism(s): Bacillus subtilis subsp. subtilis str. 168
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2021-02-24 Released: 2022-03-09
Deposition Author(s): Hamill, C.J., Prentice, E.J., Bahl, C.D., Truebridge, I.S., Arcus, V.L.
Funding Organization(s): Marsden Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free:
0.145 (Depositor), 0.145 (DCC)
R-Value Work:
0.126 (Depositor), 0.128 (DCC)
R-Value Observed:
0.127 (Depositor)

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

Literature

Urea binding to guide rational design of mutations that influence enzyme dynamics

Hamill, C.J., Arcus, V.L., Prentice, E.J., Bahl, C., Truebridge, I.

To be published.

Macromolecule Content

Total Structure Weight: 69.56 kDa
Atom Count: 5,651
Modeled Residue Count: 559
Deposited Residue Count: 586
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oligo-1,6-glucosidase 1	A [auth B]	586	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 1 Gene Names: malL, yvdL, BSU34560 EC: 3.2.1.10
UniProt
Find proteins for O06994 (Bacillus subtilis (strain 168)) Explore O06994 Go to UniProtKB: O06994
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O06994
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain B MOL2 format, chain B mmCIF format, chain B	B	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain B Interactions & Density Focus chain B
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.145 (Depositor), 0.145 (DCC)
R-Value Work: 0.126 (Depositor), 0.128 (DCC)
R-Value Observed: 0.127 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.749	α = 90
b = 100.999	β = 113.06
c = 61.749	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
MOLREP	phasing
REFMAC	refinement
PHENIX	refinement
Coot	model building
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-03-09

Deposition Author(s):

Truebridge, I.S.

Funding Organization	Location	Grant Number
Marsden Fund	New Zealand	16-UOW-027

Revision History (Full details and data files)

Version 1.0: 2022-03-09
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, 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.