4B29 | pdb_00004b29

Crystal structures of DMSP lyases RdDddP and RnDddQII

PDB DOI: https://doi.org/10.2210/pdb4B29/pdb

Classification: HYDROLASE
Organism(s): Roseovarius nubinhibens ISM
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-07-12 Released: 2012-07-25
Deposition Author(s): Hehemann, J.H., Law, A., Redecke, L., Boraston, A.B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free:
0.176 (Depositor), 0.180 (DCC)
R-Value Work:
0.162 (Depositor), 0.160 (DCC)
R-Value Observed:
0.162 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structures of Dmsp Lyases Rddddp and Rndddqii

Hehemann, J.H., Law, A., Redecke, L., Boraston, A.B.

To be published.

Macromolecule Content

Total Structure Weight: 25.3 kDa
Atom Count: 1,876
Modeled Residue Count: 195
Deposited Residue Count: 217
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DIMETHYLSULFONIOPROPIONATE LYASE	A	217	Roseovarius nubinhibens ISM	Mutation(s): 0
UniProt
Find proteins for A3SNG1 (Roseovarius nubinhibens (strain ATCC BAA-591 / DSM 15170 / ISM)) Explore A3SNG1 Go to UniProtKB: A3SNG1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A3SNG1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], D [auth A], E [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]
BR Query on BR Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A], I [auth A], L [auth A], M [auth A]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth A] Focus chain M [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free: 0.176 (Depositor), 0.180 (DCC)
R-Value Work: 0.162 (Depositor), 0.160 (DCC)
R-Value Observed: 0.162 (Depositor)

Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.54	α = 90
b = 145.54	β = 90
c = 145.54	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
SHELX	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-07-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-07-25
Type: Initial release
Version 1.1: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other