8TRF | pdb_00008trf

Crystal structure of SM0281, an alpha/beta hydrolase from Sinorhizobium meliloti

PDB DOI: https://doi.org/10.2210/pdb8TRF/pdb

Classification: HYDROLASE
Organism(s): Sinorhizobium meliloti 1021
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-08-09 Released: 2025-02-12
Deposition Author(s): Stogios, P.J., Evdokimova, E., Lemak, S., Edwards, E., Yakunin, A., Savchenko, A.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.46 Å
R-Value Free:
0.242 (Depositor), 0.243 (DCC)
R-Value Work:
0.198 (Depositor), 0.198 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of SM0281, an alpha/beta hydrolase from Sinorhizobium meliloti

Lemak, S.

To be published.

Macromolecule Content

Total Structure Weight: 126.03 kDa
Atom Count: 8,280
Modelled Residue Count: 1,009
Deposited Residue Count: 1,120
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AB hydrolase-1 domain-containing protein	A, B, C, D	280	Sinorhizobium meliloti 1021	Mutation(s): 0 Gene Names: SMc00361 EC: 3.1.2.22 (UniProt), 3.1.1.93 (UniProt)
UniProt
Find proteins for Q92KS5 (Rhizobium meliloti (strain 1021)) Explore Q92KS5 Go to UniProtKB: Q92KS5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q92KS5
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PE3 Query on PE3 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain J [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	F [auth A], G [auth A], J [auth A], K [auth B], L [auth B]	3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL C₂₈ H₅₈ O₁₅ ILLKMACMBHTSHP-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain O [auth C] MOL2 format, chain E [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain O [auth C] mmCIF format, chain E [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain O [auth C]	E [auth A], H [auth A], I [auth A], M [auth B], O [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain O [auth C] Interactions & Density Focus chain E [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain O [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B] mmCIF format, chain N [auth B]	N [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]