7KMO | pdb_00007kmo

Crystal structure of the GH35 beta-galactosidase (Xac1772) from Xanthomonas citri in complex with galactose

PDB DOI: https://doi.org/10.2210/pdb7KMO/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: 1.75 Å
R-Value Free:
0.241 (Depositor), 0.237 (DCC)
R-Value Work:
0.193 (Depositor), 0.193 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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: 60.48 kDa
Atom Count: 4,598
Modeled Residue Count: 511
Deposited Residue Count: 534
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-galactosidase, GH35	A	534	Xanthomonas citri subsp. citri 306	Mutation(s): 0 Gene Names: XAC1772

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GLA (Subject of Investigation/LOI) Query on GLA 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]	alpha-D-galactopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PHYPRBDBSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions 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] Interactions & Density 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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.241 (Depositor), 0.237 (DCC)
R-Value Work: 0.193 (Depositor), 0.193 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.68	α = 90
b = 116.68	β = 90
c = 97.77	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):

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: 2023-10-18
Changes: Data collection, Database references, Refinement description