5CU1 | pdb_00005cu1

Crystal structure of DMSP lyase DddQ from Ruegeria pomeroyi DSS-3

PDB DOI: https://doi.org/10.2210/pdb5CU1/pdb

Classification: LYASE
Organism(s): Ruegeria pomeroyi DSS-3
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-07-24 Released: 2016-08-17
Deposition Author(s): Chong, S.Y., Moran, M.A., Lanzilotta, W.N., Whitman, W.B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.267 (Depositor), 0.255 (DCC)
R-Value Work:
0.216 (Depositor), 0.235 (DCC)
R-Value Observed:
0.219 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

To be Published

Chong, S.Y., Lanzilotta, W.N.

To be published.

Macromolecule Content

Total Structure Weight: 23.42 kDa
Atom Count: 1,590
Modeled Residue Count: 197
Deposited Residue Count: 212
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DMSP lyase	A	212	Ruegeria pomeroyi DSS-3	Mutation(s): 0 Gene Names: dddQ, SPO1596 EC: 4.4.1.3
UniProt
Find proteins for Q5LT18 (Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3)) Explore Q5LT18 Go to UniProtKB: Q5LT18
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5LT18
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.267 (Depositor), 0.255 (DCC)
R-Value Work: 0.216 (Depositor), 0.235 (DCC)
R-Value Observed: 0.219 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.582	α = 90
b = 69.878	β = 90
c = 49.731	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
HKL-2000	data scaling
HKL-2000	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-08-17

Deposition Author(s):

Lanzilotta, W.N.

Revision History (Full details and data files)

Version 1.0: 2016-08-17
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description

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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.