5DPM | pdb_00005dpm

Crystal structure of UbiG mutant in complex with SAH

PDB DOI: https://doi.org/10.2210/pdb5DPM/pdb

Classification: TRANSFERASE
Organism(s): Escherichia coli HS
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-09-13 Released: 2016-09-21
Deposition Author(s): Zhu, Y., Jiang, X., Li, X., Teng, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.215 (Depositor), 0.208 (DCC)
R-Value Work:
0.176 (Depositor), 0.180 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of UbiG mutant in complex with SAH at 2.1 angstroms resolution

Zhu, Y., Jiang, X., Li, X., Teng, M.

To be published.

Macromolecule Content

Total Structure Weight: 25.4 kDa
Atom Count: 1,664
Modeled Residue Count: 206
Deposited Residue Count: 225
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquinone biosynthesis O-methyltransferase	A	225	Escherichia coli HS	Mutation(s): 0 Gene Names: ubiG, EcHS_A2372 EC: 2.1.1.222 (PDB Primary Data), 2.1.1.64 (PDB Primary Data)
UniProt
Find proteins for P17993 (Escherichia coli (strain K12)) Explore P17993 Go to UniProtKB: P17993
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P17993
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH 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]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.215 (Depositor), 0.208 (DCC)
R-Value Work: 0.176 (Depositor), 0.180 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.842	α = 90
b = 39.326	β = 94.34
c = 40.112	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-09-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-09-21
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, 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.