8I0J | pdb_00008i0j

JB13GH39P28 mutant-D41G

PDB DOI: https://doi.org/10.2210/pdb8I0J/pdb

Classification: HYDROLASE
Organism(s): Sphingomonas sp.
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2023-01-11 Released: 2024-04-24
Deposition Author(s): Zhou, J.P., Cao, L.J., Lin, M.Y., Zhang, R., Huang, Z.X.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.44 Å
R-Value Free:
0.184 (Depositor), 0.192 (DCC)
R-Value Work:
0.144 (Depositor), 0.155 (DCC)
R-Value Observed:
0.146 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

beta-Xylosidase JB13GH39P28 (D41G) showing salt/ethanol/trypsin tolerance and transformation of notoginsenosides

Cao, L.J., Lin, M.Y., Zhang, R., Huang, Z.X., Zhou, J.P.

To be published.

Macromolecule Content

Total Structure Weight: 116.62 kDa
Atom Count: 8,773
Modeled Residue Count: 988
Deposited Residue Count: 1,040
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoside hydrolase family 39 beta-xylosidase	A, B	520	Sphingomonas sp.	Mutation(s): 1
UniProt
Find proteins for A0ACD6B930 (Sphingomonas sp) Explore A0ACD6B930 Go to UniProtKB: A0ACD6B930
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6B930
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL (Subject of Investigation/LOI) Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.44 Å
R-Value Free: 0.184 (Depositor), 0.192 (DCC)
R-Value Work: 0.144 (Depositor), 0.155 (DCC)
R-Value Observed: 0.146 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.132	α = 90
b = 63.64	β = 93.76
c = 144.303	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-04-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded	China	--

Revision History (Full details and data files)

Version 1.0: 2024-04-24
Type: Initial release

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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.