8YYO | pdb_00008yyo

Crystal structure of TsaGH11 complexed with beta-D-xylopyranose (Data II)

PDB DOI: https://doi.org/10.2210/pdb8YYO/pdb

Classification: HYDROLASE
Organism(s): Thermoanaerobacterium saccharolyticum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-04-04 Released: 2024-04-17
Deposition Author(s): Nam, K.H.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.194 (Depositor), 0.190 (DCC)
R-Value Work:
0.165 (Depositor), 0.160 (DCC)
R-Value Observed:
0.166 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Recognition of a Single Beta-D-Xylopyranose Molecule by Xylanase GH11 from Thermoanaerobacterium saccharolyticum.

(2024) Crystals (Basel) 14

DOI: https://doi.org/10.3390/cryst14050402

Macromolecule Content

Total Structure Weight: 40.69 kDa
Atom Count: 3,284
Modeled Residue Count: 366
Deposited Residue Count: 368
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endo-1,4-beta-xylanase	A, B	184	Thermoanaerobacterium saccharolyticum	Mutation(s): 0 Gene Names: Tsac_0897 EC: 3.2.1.8
UniProt
Find proteins for I3VTR8 (Thermoanaerobacterium saccharolyticum (strain DSM 8691 / JW/SL-YS485)) Explore I3VTR8 Go to UniProtKB: I3VTR8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I3VTR8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XYP (Subject of Investigation/LOI) Query on XYP Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A]	D [auth A], E [auth B]	beta-D-xylopyranose C₅ H₁₀ O₅ SRBFZHDQGSBBOR-KKQCNMDGSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth B]
ACT Query on ACT 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]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.194 (Depositor), 0.190 (DCC)
R-Value Work: 0.165 (Depositor), 0.160 (DCC)
R-Value Observed: 0.166 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.226	α = 90
b = 73.226	β = 90
c = 164.778	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-04-17

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2021R1I1A1A01050838

Revision History (Full details and data files)

Version 1.0: 2024-04-17
Type: Initial release
Version 1.1: 2024-10-30
Changes: Database references, Structure summary

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.