7CBE | pdb_00007cbe

Crystal structure of Homoserine O-succinyltransferase from Escherichia coli K-12

PDB DOI: https://doi.org/10.2210/pdb7CBE/pdb

Classification: TRANSFERASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2020-06-12 Released: 2021-06-16
Deposition Author(s): Sagong, H.-Y., Kim, K.-J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.251 (Depositor), 0.258 (DCC)
R-Value Work:
0.225 (Depositor), 0.233 (DCC)
R-Value Observed:
0.226 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of Homoserine O-succinyltransferase from Escherichia coli K-12

Sagong, H.-Y., Kim, K.-J.

To be published.

Macromolecule Content

Total Structure Weight: 71.87 kDa
Atom Count: 4,950
Modeled Residue Count: 575
Deposited Residue Count: 618
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Homoserine O-succinyltransferase	A, B	309	Escherichia coli K-12	Mutation(s): 0 Gene Names: metAS, metA, b4013, JW3973 EC: 2.3.1.46
UniProt
Find proteins for P07623 (Escherichia coli (strain K12)) Explore P07623 Go to UniProtKB: P07623
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07623
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
EDO Query on EDO 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]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.251 (Depositor), 0.258 (DCC)
R-Value Work: 0.225 (Depositor), 0.233 (DCC)
R-Value Observed: 0.226 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.348	α = 90
b = 81.027	β = 90
c = 98.093	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
MOLREP	phasing
HKL-2000	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2021-06-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-06-16
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Database references, 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.