3LWS | pdb_00003lws

Crystal structure of Putative aromatic amino acid beta-eliminating lyase/threonine aldolase. (YP_001813866.1) from Exiguobacterium sp. 255-15 at 2.00 A resolution

PDB DOI: https://doi.org/10.2210/pdb3LWS/pdb

Classification: LYASE
Organism(s): Exiguobacterium artemiae 255-15
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-02-24 Released: 2010-03-31
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.190 (Depositor), 0.190 (DCC)
R-Value Work:
0.144 (Depositor), 0.150 (DCC)
R-Value Observed:
0.146 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of Putative aromatic amino acid beta-eliminating lyase/threonine aldolase. (YP_001813866.1) from Exiguobacterium sp. 255-15 at 2.00 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 241.76 kDa
Atom Count: 18,270
Modeled Residue Count: 2,130
Deposited Residue Count: 2,142
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aromatic amino acid beta-eliminating lyase/threonine aldolase	A, B, C, D, E A, B, C, D, E, F	357	Exiguobacterium artemiae 255-15	Mutation(s): 0 Gene Names: Exig_1379
UniProt
Find proteins for B1YFH3 (Exiguobacterium sibiricum (strain DSM 17290 / CCUG 55495 / CIP 109462 / JCM 13490 / 255-15)) Explore B1YFH3 Go to UniProtKB: B1YFH3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B1YFH3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.190 (Depositor), 0.190 (DCC)
R-Value Work: 0.144 (Depositor), 0.150 (DCC)
R-Value Observed: 0.146 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33LWS

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.15	α = 90
b = 142.15	β = 90
c = 102.71	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-03-31

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2010-03-31
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.3: 2019-07-17
Changes: Advisory, Data collection, Derived calculations, Refinement description
Version 1.4: 2023-02-01
Changes: Database references

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.