7KNC | pdb_00007knc

Crystal structure of the GH31 alpha-xylosidase (Xac1773) from Xanthomonas citri

PDB DOI: https://doi.org/10.2210/pdb7KNC/pdb

Classification: HYDROLASE
Organism(s): Xanthomonas citri subsp. citri 306
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2020-11-04 Released: 2021-05-26
Deposition Author(s): Vieira, P.S., Murakami, M.T.
Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.87 Å
R-Value Free:
0.225 (Depositor), 0.226 (DCC)
R-Value Work:
0.191 (Depositor), 0.192 (DCC)
R-Value Observed:
0.193 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Xyloglucan processing machinery in Xanthomonas pathogens and its role in the transcriptional activation of virulence factors

Vieira, P.S., Bonfim, I.M., Araujo, E.A., Melo, R.R., Lima, A.R., Fessel, M.R., Paixao, D.A.A., Persinoti, G.F., Rocco, S.A., Lima, T.B., Pirolla, R.A.S., Morais, M.A.B., Correa, J.B.L., Zanphorlin, L.M., Diogo, J.A., Lima, E.A., Grandis, A., Buckeridge, M.S., Gozzo, F.C., Benedetti, C.E., Polikarpov, I., Giuseppe, P.O., Murakami, M.T.

(2021) Nature Communications 12: 4049

DOI: https://doi.org/10.1038/s41467-021-24277-4

Macromolecule Content

Total Structure Weight: 111.33 kDa
Atom Count: 8,159
Modeled Residue Count: 919
Deposited Residue Count: 988
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-xylosidase	A	988	Xanthomonas citri subsp. citri 306	Mutation(s): 1 Gene Names: xylS, XAC1773

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XYS (Subject of Investigation/LOI) Query on XYS 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]	alpha-D-xylopyranose C₅ H₁₀ O₅ SRBFZHDQGSBBOR-LECHCGJUSA-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 D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
K Query on K 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]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.87 Å
R-Value Free: 0.225 (Depositor), 0.226 (DCC)
R-Value Work: 0.191 (Depositor), 0.192 (DCC)
R-Value Observed: 0.193 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.493	α = 90
b = 146.632	β = 90
c = 63.044	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-05-26

Deposition Author(s):

Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	2016/06509-0
Sao Paulo Research Foundation (FAPESP)	Brazil	2015/26982-0

Revision History (Full details and data files)

Version 1.0: 2021-05-26
Type: Initial release
Version 1.1: 2021-07-07
Changes: Database references
Version 1.2: 2023-10-18
Changes: Data collection, Database references, Refinement description

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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.