3LZA | pdb_00003lza

Crystal structure of Putative SnoaL-like polyketide cyclase (YP_563807.1) from SHEWANELLA DENITRIFICANS OS-217 at 1.70 A resolution

PDB DOI: https://doi.org/10.2210/pdb3LZA/pdb

Classification: LYASE
Organism(s): Shewanella denitrificans OS217
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-03-01 Released: 2010-05-12
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.238 (Depositor), 0.248 (DCC)
R-Value Work:
0.193 (Depositor), 0.209 (DCC)
R-Value Observed:
0.195 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3LZA

This is version 1.5 of the entry. See complete history.

Literature

CRYSTAL STRUCTURE OF PUTATIVE SNOAL-LIKE POLYKETIDE CYCLASE (YP_563807.1) FROM SHEWANELLA DENITRIFICANS OS-217 AT 1.70 A RESOLUTION

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 65.19 kDa
Atom Count: 5,149
Modeled Residue Count: 547
Deposited Residue Count: 564
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative SnoaL-like polyketide cyclase	A, B, C, D	141	Shewanella denitrificans OS217	Mutation(s): 0 Gene Names: YP_563807.1, Sden_2805
UniProt
Find proteins for Q12KE2 (Shewanella denitrificans (strain OS217 / ATCC BAA-1090 / DSM 15013)) Explore Q12KE2 Go to UniProtKB: Q12KE2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q12KE2
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.238 (Depositor), 0.248 (DCC)
R-Value Work: 0.193 (Depositor), 0.209 (DCC)
R-Value Observed: 0.195 (Depositor)

Diffraction Data:

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.843	α = 90.13
b = 56.51	β = 103.27
c = 57.537	γ = 102.85

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-05-12

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2010-05-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-02-01
Changes: Database references
Version 1.5: 2024-11-27
Changes: Data collection, 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.