4BOJ | pdb_00004boj

Crystal structure of Bacillus circulans TN-31 Aman6 in complex with mannobiose

PDB DOI: https://doi.org/10.2210/pdb4BOJ/pdb

Classification: HYDROLASE
Organism(s): Niallia circulans
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2013-05-21 Released: 2014-05-28
Deposition Author(s): Striebeck, A., van Aalten, D.M.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.38 Å
R-Value Free:
0.191 (Depositor), 0.193 (DCC)
R-Value Work:
0.171 (Depositor), 0.173 (DCC)
R-Value Observed:
0.172 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4BOJ

This is version 2.1 of the entry. See complete history.

Literature

The Structure of B. Circulans Aman6 Defines the Fold and Mechanism of the Gh-76 Mannoprotein Transglycosylases and Bacterial Mannosidases

Striebeck, A., Borodkin, V.S., Ferenbach, A.T., Van Aalten, D.M.F.

To be published.

Macromolecule Content

Total Structure Weight: 117.56 kDa
Atom Count: 9,247
Modeled Residue Count: 1,010
Deposited Residue Count: 1,032
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA-1,6-MANNANASE	A, B, C	344	Niallia circulans	Mutation(s): 1
UniProt
Find proteins for Q9Z4P9 (Niallia circulans) Explore Q9Z4P9 Go to UniProtKB: Q9Z4P9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Z4P9
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose	D, E, F	2		N/A	Interactions Focus chain D Focus chain E Focus chain F Interactions & Density Focus chain D Focus chain E Focus chain F
Glycosylation Resources
GlyTouCan: G77384RA GlyCosmos: G77384RA GlyGen: G77384RA

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900118 Query on PRD_900118	D, E, F	6alpha-alpha-mannobiose	Oligosaccharide / Metabolism		Interactions Focus chain D Focus chain E Focus chain F Interactions & Density Focus chain D Focus chain E Focus chain F

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.38 Å
R-Value Free: 0.191 (Depositor), 0.193 (DCC)
R-Value Work: 0.171 (Depositor), 0.173 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.63	α = 90
b = 114.14	β = 90
c = 134.41	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-05-28

Deposition Author(s):

van Aalten, D.M.F.

Revision History (Full details and data files)

Version 1.0: 2014-05-28
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 2.1: 2024-05-08
Changes: Data collection, Database references, Structure summary

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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.