3JUG | pdb_00003jug

Crystal structure of endo-beta-1,4-mannanase from the alkaliphilic Bacillus sp. N16-5

PDB DOI: https://doi.org/10.2210/pdb3JUG/pdb

Classification: HYDROLASE
Organism(s): Bacillus sp. N16-5
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-09-15 Released: 2010-09-15
Deposition Author(s): Zhao, Y., Zhang, Y., Xue, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.215 (Depositor), 0.175 (DCC)
R-Value Work:
0.174 (Depositor)
R-Value Observed:
0.176 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 3JUG

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

Literature

Structure Analysis of Alkaline beta-mannanase from Alkaliphilic Bacillus sp. N16-5 Implications for Adaptation to Alkaline Conditions

Zhao, Y., Zhang, Y., Cao, Y., Qi, J., Xue, Y., Gao, F., Peng, H., Gao, G.F., Ma, Y.

To be published.

Macromolecule Content

Total Structure Weight: 38.26 kDa
Atom Count: 2,905
Modeled Residue Count: 294
Deposited Residue Count: 345
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-mannanase	A	345	Bacillus sp. N16-5	Mutation(s): 0 Gene Names: manA EC: 3.2.1.78
UniProt
Find proteins for Q5YEX6 (Bacillus sp. N16-5) Explore Q5YEX6 Go to UniProtKB: Q5YEX6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5YEX6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 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]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.215 (Depositor), 0.175 (DCC)
R-Value Work: 0.174 (Depositor)
R-Value Observed: 0.176 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.033	α = 90
b = 63.312	β = 90
c = 83.342	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-09-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-09-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.