3BYK

Crystal structure of B. subtilis levansucrase mutant D247A

PDB DOI: https://doi.org/10.2210/pdb3BYK/pdb

Classification: TRANSFERASE
Organism(s): Bacillus subtilis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2008-01-16 Released: 2008-02-12
Deposition Author(s): Futterer, K., Meng, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.215 (Depositor), 0.220 (DCC)
R-Value Work:
0.169 (Depositor), 0.180 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Donor substrate recognition in the raffinose-bound E342A mutant of fructosyltransferase Bacillus subtilis levansucrase

Meng, G., Futterer, K.

To be published.

Macromolecule Content

Total Structure Weight: 53.03 kDa
Atom Count: 3,711
Modelled Residue Count: 440
Deposited Residue Count: 473
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Levansucrase	A	473	Bacillus subtilis	Mutation(s): 1 Gene Names: SACB EC: 2.4.1.10
UniProt
Find proteins for P05655 (Bacillus subtilis (strain 168)) Explore P05655 Go to UniProtKB: P05655
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P05655
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA 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]	CALCIUM ION Ca BHPQYMZQTOCNFJ-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: 2.10 Å
R-Value Free: 0.215 (Depositor), 0.220 (DCC)
R-Value Work: 0.169 (Depositor), 0.180 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.158	α = 90
b = 67.351	β = 90
c = 123.792	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-02-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-02-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2021-11-10
Changes: Database references, Derived calculations
Version 1.3: 2023-11-01
Changes: Data collection, Refinement description

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.