3PNX | pdb_00003pnx

Crystal structure of a putative sulfurtransferase dsrE (Swol_2425) from Syntrophomonas wolfei str. Goettingen at 1.92 A resolution

PDB DOI: https://doi.org/10.2210/pdb3PNX/pdb

Classification: TRANSFERASE
Organism(s): Syntrophomonas wolfei subsp. wolfei str. Goettingen G311
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-11-19 Released: 2010-12-15
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free:
0.215 (Depositor), 0.218 (DCC)
R-Value Work:
0.190 (Depositor), 0.194 (DCC)
R-Value Observed:
0.191 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3PNX

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

Literature

Crystal structure of a putative sulfurtransferase dsrE (Swol_2425) from Syntrophomonas wolfei str. Goettingen at 1.92 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 112.87 kDa
Atom Count: 7,805
Modeled Residue Count: 948
Deposited Residue Count: 960
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative sulfurtransferase dsrE	A, B, C, D, E A, B, C, D, E, F	160	Syntrophomonas wolfei subsp. wolfei str. Goettingen G311	Mutation(s): 0 Gene Names: Swol_2425
UniProt
Find proteins for Q0AU90 (Syntrophomonas wolfei subsp. wolfei (strain DSM 2245B / Goettingen)) Explore Q0AU90 Go to UniProtKB: Q0AU90
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q0AU90
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain S [auth D] SDF format, chain M [auth B] SDF format, chain K [auth A] MOL2 format, chain T [auth D] MOL2 format, chain S [auth D] MOL2 format, chain M [auth B] MOL2 format, chain K [auth A] mmCIF format, chain T [auth D] mmCIF format, chain S [auth D] mmCIF format, chain M [auth B] mmCIF format, chain K [auth A]	K [auth A], M [auth B], S [auth D], T [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain M [auth B] Focus chain S [auth D] Focus chain T [auth D] Interactions & Density Focus chain K [auth A] Focus chain M [auth B] Focus chain S [auth D] Focus chain T [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain G [auth A] MOL2 format, chain O [auth D] MOL2 format, chain G [auth A] mmCIF format, chain O [auth D] mmCIF format, chain G [auth A]	G [auth A], O [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain O [auth D] Interactions & Density Focus chain G [auth A] Focus chain O [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain V [auth F] SDF format, chain U [auth E] SDF format, chain R [auth D] SDF format, chain Q [auth D] SDF format, chain P [auth D] SDF format, chain N [auth C] SDF format, chain L [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain V [auth F] MOL2 format, chain U [auth E] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain P [auth D] MOL2 format, chain N [auth C] MOL2 format, chain L [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain V [auth F] mmCIF format, chain U [auth E] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain P [auth D] mmCIF format, chain N [auth C] mmCIF format, chain L [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A] I [auth A] J [auth A] L [auth B] N [auth C] H [auth A], I [auth A], J [auth A], L [auth B], N [auth C], P [auth D], Q [auth D], R [auth D], U [auth E], V [auth F]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D] Focus chain U [auth E] Focus chain V [auth F] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D] Focus chain U [auth E] Focus chain V [auth F]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET
OCS Query on OCS	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₃ H₇ N O₅ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free: 0.215 (Depositor), 0.218 (DCC)
R-Value Work: 0.190 (Depositor), 0.194 (DCC)
R-Value Observed: 0.191 (Depositor)

Diffraction Data:

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.416	α = 90
b = 76.504	β = 93.08
c = 127.652	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-12-15

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2010-12-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2011-07-20
Changes: Structure summary
Version 1.3: 2017-10-25
Changes: Author supporting evidence
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations

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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.