3KXR

Structure of the cystathionine beta-synthase pair domain of the putative Mg2+ transporter SO5017 from Shewanella oneidensis MR-1.

PDB DOI: https://doi.org/10.2210/pdb3KXR/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Shewanella oneidensis MR-1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-12-03 Released: 2009-12-15
Deposition Author(s): Fratczak, Z., Zimmerman, M.D., Chruszcz, M., Cymborowski, M., Kagan, O., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free: 0.228
R-Value Work: 0.190
R-Value Observed: 0.191

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structure of the cystathionine beta-synthase pair domain of the putative Mg2+ transporter SO5017 from Shewanella oneidensis MR-1.

Fratczak, Z., Zimmerman, M.D., Chruszcz, M., Cymborowski, M., Kagan, O., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W.

To be published.

Macromolecule Content

Total Structure Weight: 23.82 kDa
Atom Count: 1,396
Modelled Residue Count: 171
Deposited Residue Count: 205
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Magnesium transporter, putative	A	205	Shewanella oneidensis MR-1	Mutation(s): 0 Gene Names: SO_1565
UniProt
Find proteins for Q8EGN5 (Shewanella oneidensis (strain MR-1)) Explore Q8EGN5 Go to UniProtKB: Q8EGN5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8EGN5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A]	B [auth A], C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free: 0.228
R-Value Work: 0.190
R-Value Observed: 0.191
Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.596	α = 90
b = 103.596	β = 90
c = 134.302	γ = 120

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-3000	phasing
MLPHARE	phasing
DM	model building
SHELXD	phasing
ARP/wARP	model building
CCP4	model building
REFMAC	refinement
Coot	model building
HKL-3000	data reduction
HKL-2000	data scaling
DM	phasing
CCP4	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-12-15

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2009-12-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2022-04-13
Changes: Database references, Derived calculations, Structure summary

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Help and Resources

3KXR

Structure of the cystathionine beta-synthase pair domain of the putative Mg2+ transporter SO5017 from Shewanella oneidensis MR-1.

Structure of the cystathionine beta-synthase pair domain of the putative Mg2+ transporter SO5017 from Shewanella oneidensis MR-1.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)