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), 0.192 (DCC)
R-Value Work:
0.144 (Depositor), 0.147 (DCC)
R-Value Observed:
0.146 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3LWS

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:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.192 (DCC)
R-Value Work: 0.144 (Depositor), 0.147 (DCC)
R-Value Observed: 0.146 (Depositor)

Diffraction Data:

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

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View more in-depth experimental data

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

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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.