9MS4 | pdb_00009ms4

Crystal structure of an expansin (Xa_EXLX1) from Xanthomonas sacchari

PDB DOI: https://doi.org/10.2210/pdb9MS4/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Xanthomonas sacchari
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-01-09 Released: 2025-05-21
Deposition Author(s): Smith, C.A., Buchko, G.W., Momeni, M.H., Master, E.R.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.240 (Depositor), 0.240 (DCC)
R-Value Work:
0.188 (Depositor), 0.189 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Insights into the action of phylogenetically diverse microbial expansins

Buchko, G.W., Smith, C.A., Momeni, M.H., Master, E.R.

To be published.

Macromolecule Content

Total Structure Weight: 180.97 kDa
Atom Count: 12,995
Modeled Residue Count: 1,664
Deposited Residue Count: 1,672
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Expansin (Peptidoglycan-binding protein)	A, B, C, D, E A, B, C, D, E, F, G, H	209	Xanthomonas sacchari	Mutation(s): 0 Gene Names: FHR56_002727
UniProt
Find proteins for A0AA46ST83 (Xanthomonas sacchari) Explore A0AA46ST83 Go to UniProtKB: A0AA46ST83
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0AA46ST83
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1BNY Query on A1BNY Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain N [auth D] SDF format, chain O [auth F] SDF format, chain P [auth G] MOL2 format, chain K [auth A] MOL2 format, chain N [auth D] MOL2 format, chain O [auth F] MOL2 format, chain P [auth G] mmCIF format, chain K [auth A] mmCIF format, chain N [auth D] mmCIF format, chain O [auth F] mmCIF format, chain P [auth G]	K [auth A], N [auth D], O [auth F], P [auth G]	2-hydroxy-3,5-dinitrobenzoic acid C₇ H₄ N₂ O₇ LWFUFLREGJMOIZ-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain N [auth D] Focus chain O [auth F] Focus chain P [auth G] Interactions & Density Focus chain K [auth A] Focus chain N [auth D] Focus chain O [auth F] Focus chain P [auth G]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain L [auth C] SDF format, chain M [auth D] SDF format, chain Q [auth G] SDF format, chain R [auth H] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth C] MOL2 format, chain M [auth D] MOL2 format, chain Q [auth G] MOL2 format, chain R [auth H] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain L [auth C] mmCIF format, chain M [auth D] mmCIF format, chain Q [auth G] mmCIF format, chain R [auth H]	I [auth A] J [auth A] L [auth C] M [auth D] Q [auth G] I [auth A], J [auth A], L [auth C], M [auth D], Q [auth G], R [auth H]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth C] Focus chain M [auth D] Focus chain Q [auth G] Focus chain R [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth C] Focus chain M [auth D] Focus chain Q [auth G] Focus chain R [auth H]