7KMM | pdb_00007kmm

Crystal structure of XAC1771, a novel carbohydrate acetylesterase from Xanthomonas citri

PDB DOI: https://doi.org/10.2210/pdb7KMM/pdb

Classification: HYDROLASE
Organism(s): Xanthomonas citri subsp. citri 306
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-11-03 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: 1.90 Å
R-Value Free:
0.238 (Depositor), 0.243 (DCC)
R-Value Work:
0.190 (Depositor), 0.196 (DCC)
R-Value Observed:
0.192 (Depositor)

wwPDB Validation 3D Report Full Report

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: 138.27 kDa
Atom Count: 7,001
Modeled Residue Count: 867
Deposited Residue Count: 1,272
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sialic acid-specific 9-O-acetylesterase	A, B	636	Xanthomonas citri subsp. citri 306	Mutation(s): 0 Gene Names: XAC1771

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth A] SDF format, chain H [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] SDF format, chain C [auth A] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [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] MOL2 format, chain C [auth A] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [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] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] 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 B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain C [auth A] 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 B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEB Query on SEB	A, B	L-PEPTIDE LINKING	C₁₀ H₁₃ N O₅ S		SER

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.238 (Depositor), 0.243 (DCC)
R-Value Work: 0.190 (Depositor), 0.196 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.852	α = 90
b = 63.497	β = 98.15
c = 88.284	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-05-26

Deposition Author(s):

Vieira, P.S.

Murakami, M.T.

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: 2025-04-02
Changes: Data collection, Database references, Structure summary