7W2W | pdb_00007w2w

Crystal structure of TxGH116 R786K mutant from Thermoanaerobacterium xylanolyticum with glucose

PDB DOI: https://doi.org/10.2210/pdb7W2W/pdb

Classification: HYDROLASE
Organism(s): Thermoanaerobacterium xylanolyticum LX-11
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2021-11-24 Released: 2022-04-06
Deposition Author(s): Huang, M., Pengthaisong, S., Charoenwattanasatien, R., Jitonnom, J., Ketudat Cairns, J.R.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free:
0.185 (Depositor), 0.192 (DCC)
R-Value Work:
0.150 (Depositor), 0.163 (DCC)
R-Value Observed:
0.152 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Systematic Functional and Computational Analysis of Glucose-Binding Residues in Glycoside Hydrolase Family GH116.

Huang, M., Pengthaisong, S., Charoenwattanasatien, R., Thinkumrob, N., Jitonnom, J., Ketudat Cairns, J.R.

(2022) Catalysts 12

DOI: https://doi.org/10.3390/catal12030343

Macromolecule Content

Total Structure Weight: 98.23 kDa
Atom Count: 6,868
Modeled Residue Count: 771
Deposited Residue Count: 842
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucosylceramidase	A	842	Thermoanaerobacterium xylanolyticum LX-11	Mutation(s): 1 Gene Names: Thexy_2211 EC: 3.2.1.45
UniProt
Find proteins for F6BL85 (Thermoanaerobacterium xylanolyticum (strain ATCC 49914 / DSM 7097 / LX-11)) Explore F6BL85 Go to UniProtKB: F6BL85
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F6BL85
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BGC (Subject of Investigation/LOI) Query on BGC Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GLC (Subject of Investigation/LOI) Query on GLC 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]	alpha-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-DVKNGEFBSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain O [auth A] MOL2 format, chain O [auth A] mmCIF format, chain O [auth A]	O [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain O [auth A] Interactions & Density Focus chain O [auth A]
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain R [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain H [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain R [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain H [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain R [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], R [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain R [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain R [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain P [auth A] MOL2 format, chain P [auth A] mmCIF format, chain P [auth A]	P [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain P [auth A] Interactions & Density Focus chain P [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain Q [auth A]	Q [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain Q [auth A] Interactions & Density Focus chain Q [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free: 0.185 (Depositor), 0.192 (DCC)
R-Value Work: 0.150 (Depositor), 0.163 (DCC)
R-Value Observed: 0.152 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 177.285	α = 90
b = 54.463	β = 90
c = 83.074	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-04-06

Deposition Author(s):

Huang, M.

Pengthaisong, S.

Charoenwattanasatien, R.

Jitonnom, J.

Ketudat Cairns, J.R.

Funding Organization	Location	Grant Number
Other government	Thailand	Suranaree University of Technology
Other government	Thailand	Thailand Research Fund
Other government	Thailand	Thailand Science Research and Innovation
Other government	Thailand	Synchrotron Light Research Institute (Public Organization)
Other government	Thailand	University of Phayao