6JDT | pdb_00006jdt

Crystal structure of GH10 family xylanase XynAF1 from Aspergillus fumigatus Z5

PDB DOI: https://doi.org/10.2210/pdb6JDT/pdb

Classification: HYDROLASE
Organism(s): Aspergillus fumigatus Z5
Expression System: Komagataella pastoris
Mutation(s): No

Deposited: 2019-02-02 Released: 2020-05-20
Deposition Author(s): Li, G., Miao, Y., Zhang, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.68 Å
R-Value Free:
0.168 (Depositor), 0.177 (DCC)
R-Value Work:
0.136 (Depositor), 0.149 (DCC)
R-Value Observed:
0.137 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

Crystal structure of GH10 family xylanase XynAF1 from Aspergillus fumigatus Z5

Li, G., Miao, Y., Zhang, R.

To be published.

Macromolecule Content

Total Structure Weight: 69.34 kDa
Atom Count: 5,414
Modeled Residue Count: 638
Deposited Residue Count: 638
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-xylanase	A, B	319	Aspergillus fumigatus Z5	Mutation(s): 0 Gene Names: Y699_04481 EC: 3.2.1.8

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 E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.68 Å
R-Value Free: 0.168 (Depositor), 0.177 (DCC)
R-Value Work: 0.136 (Depositor), 0.149 (DCC)
R-Value Observed: 0.137 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.606	α = 73.86
b = 57.575	β = 80.39
c = 65.088	γ = 68.35

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-05-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-05-20
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.2: 2024-11-13
Changes: Data collection, Database references, 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.