3LAZ | pdb_00003laz

The crystal structure of the N-terminal domain of D-galactarate dehydratase from Escherichia coli CFT073

PDB DOI: https://doi.org/10.2210/pdb3LAZ/pdb

Classification: LYASE
Organism(s): Escherichia coli CFT073
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-01-07 Released: 2010-01-19
Deposition Author(s): Tan, K., Li, H., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free:
0.245 (Depositor), 0.247 (DCC)
R-Value Work:
0.203 (Depositor), 0.205 (DCC)
R-Value Observed:
0.205 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

The crystal structure of the N-terminal domain of D-galactarate dehydratase from Escherichia coli CFT073

Tan, K., Li, H., Bearden, J., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 21.91 kDa
Atom Count: 1,569
Modelled Residue Count: 192
Deposited Residue Count: 198
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-galactarate dehydratase	A, B	99	Escherichia coli CFT073	Mutation(s): 0 Gene Names: c3883, yhaG EC: 4.2.1.42
UniProt
Find proteins for P39829 (Escherichia coli (strain K12)) Explore P39829 Go to UniProtKB: P39829
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P39829
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

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: 1.92 Å
R-Value Free: 0.245 (Depositor), 0.247 (DCC)
R-Value Work: 0.203 (Depositor), 0.205 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.279	α = 90
b = 106.279	β = 90
c = 51.389	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP	model building
WARP	model building
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-01-19

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2010-01-19
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary

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.