4YN5 | pdb_00004yn5

Catalytic domain of Bacillus sp. JAMB-750 GH26 Endo-beta-1,4-mannanase

PDB DOI: https://doi.org/10.2210/pdb4YN5/pdb

Classification: HYDROLASE
Organism(s): Bacillus sp. JAMB750
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2015-03-09 Released: 2016-03-09
Deposition Author(s): Shimane, Y., Ohta, Y., Usami, R., Hatada, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.249 (Depositor), 0.222 (DCC)
R-Value Work:
0.200 (Depositor)
R-Value Observed:
0.203 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4YN5

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

Literature

Crystal structure of Bacillus sp. JAMB-750 GH26 Endo-beta-1,4-mannanase

Shimane, Y., Takeda, N., Ohta, Y., Kumasaka, T., Shimamura, S., Minegishi, H., Usami, R., Hatada, Y.

To be published.

Macromolecule Content

Total Structure Weight: 49.79 kDa
Atom Count: 3,360
Modeled Residue Count: 391
Deposited Residue Count: 442
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mannan endo-1,4-beta-mannosidase	A	442	Bacillus sp. JAMB750	Mutation(s): 0 Gene Names: man26A
UniProt
Find proteins for Q2ACI1 (Bacillus sp. JAMB750) Explore Q2ACI1 Go to UniProtKB: Q2ACI1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2ACI1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CAC Query on CAC 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]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.249 (Depositor), 0.222 (DCC)
R-Value Work: 0.200 (Depositor)
R-Value Observed: 0.203 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.403	α = 90
b = 124.403	β = 90
c = 45.786	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-03-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-03-09
Type: Initial release
Version 1.1: 2020-01-29
Changes: Data collection, Database references, Derived calculations
Version 1.2: 2024-03-20
Changes: Data collection, Database references

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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.