1YW6 | pdb_00001yw6

Crystal Structure of Succinylglutamate Desuccinylase from Escherichia coli, Northeast Structural Genomics Target ET72.

PDB DOI: https://doi.org/10.2210/pdb1YW6/pdb

Classification: HYDROLASE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2005-02-17 Released: 2005-03-08
Deposition Author(s): Forouhar, F., Yong, W., Kuzin, A.P., Ciano, M., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free:
0.289 (Depositor), 0.284 (DCC)
R-Value Work:
0.227 (Depositor), 0.233 (DCC)
R-Value Observed:
0.227 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1YW6

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of Succinylglutamate Desuccinylase from Escherichia coli, Northeast Structural Genomics Target ET72.

Forouhar, F., Yong, W., Kuzin, A.P., Ciano, M., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 75.81 kDa
Atom Count: 4,969
Modeled Residue Count: 619
Deposited Residue Count: 670
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinylglutamate desuccinylase	A, B	335	Escherichia coli	Mutation(s): 8 Gene Names: astE EC: 3.1 (PDB Primary Data), 3.5.1.96 (UniProt)
UniProt
Find proteins for P76215 (Escherichia coli (strain K12)) Explore P76215 Go to UniProtKB: P76215
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P76215
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.289 (Depositor), 0.284 (DCC)
R-Value Work: 0.227 (Depositor), 0.233 (DCC)
R-Value Observed: 0.227 (Depositor)

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.804	α = 90
b = 146.804	β = 90
c = 209.449	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2005-03-08

Deposition Author(s):

Montelione, G.T.

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2005-03-08
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary

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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.