Macromolecule Content

Total Structure Weight: 273.21 kDa
Atom Count: 19,228
Modelled Residue Count: 2,457
Deposited Residue Count: 2,464
Unique protein chains: 1

3LK6

Beta-N-hexosaminidase N318D mutant (YBBD_N318D) from bacillus subtilis

PDB DOI: https://doi.org/10.2210/pdb3LK6/pdb

Classification: HYDROLASE
Organism(s): Bacillus subtilis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2010-01-27 Released: 2011-05-25
Deposition Author(s): Krug, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.88 Å
R-Value Free: 0.201
R-Value Work: 0.171
R-Value Observed: 0.173

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Beta-N-hexosaminidase N318D mutant (YBBD_N318D) from bacillus subtilis

Krug, M., Fischer, S., Diederichs, K., Boos, W., Mayer, C.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipoprotein ybbD	A, B, C, D	616	Bacillus subtilis	Mutation(s): 1 Gene Names: BSU01660, ybbD, yzbA EC: 3.2.1.52
UniProt
Find proteins for P40406 (Bacillus subtilis (strain 168)) Explore P40406 Go to UniProtKB: P40406
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P40406
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D]	E [auth A] F [auth A] G [auth A] H [auth A] J [auth B] E [auth A], F [auth A], G [auth A], H [auth A], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], Q [auth C], R [auth C], S [auth C], T [auth C], U [auth C], W [auth D], X [auth D], Y [auth D], Z [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Ligand Interaction
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain I [auth A] SDF format, chain P [auth B] SDF format, chain V [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B] MOL2 format, chain V [auth C]	AA [auth D], I [auth A], P [auth B], V [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.88 Å
R-Value Free: 0.201
R-Value Work: 0.171
R-Value Observed: 0.173
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.315	α = 90.11
b = 99.149	β = 90.05
c = 139.861	γ = 89.94

Software Package:

Software Name	Purpose
XDS	data scaling
PHASER	phasing
PHENIX	refinement
XDS	data reduction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-05-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-05-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-10-13
Changes: Database references, Derived calculations

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.