7WHA | pdb_00007wha

The mutant crystal structure of b-1,4-Xylanase (XynAF1_R246K)

PDB DOI: https://doi.org/10.2210/pdb7WHA/pdb

Classification: HYDROLASE
Organism(s): Aspergillus fumigatus
Expression System: Komagataella pastoris
Mutation(s): Yes

Deposited: 2021-12-30 Released: 2023-01-25
Deposition Author(s): Li, G.Q., Zhang, R.F.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free:
0.183 (Depositor), 0.183 (DCC)
R-Value Work:
0.154 (Depositor), 0.154 (DCC)
R-Value Observed:
0.155 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

The mutant crystal structure of b-1,4-Xylanase (XynAF1_R246K)

Li, G.Q., Zhang, R.F.

To be published.

Macromolecule Content

Total Structure Weight: 70.92 kDa
Atom Count: 5,295
Modeled Residue Count: 638
Deposited Residue Count: 658
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-xylanase	A, B	329	Aspergillus fumigatus	Mutation(s): 1 Gene Names: CDV57_00377 EC: 3.2.1.8
UniProt
Find proteins for Q4WLG5 (Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293)) Explore Q4WLG5 Go to UniProtKB: Q4WLG5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4WLG5
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG 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]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free: 0.183 (Depositor), 0.183 (DCC)
R-Value Work: 0.154 (Depositor), 0.154 (DCC)
R-Value Observed: 0.155 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.165	α = 90
b = 85.939	β = 90
c = 97.831	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
REFMAC	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-01-25

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2023-01-25
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description
Version 1.2: 2024-11-06
Changes: Structure summary

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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.