6SYM | pdb_00006sym

Crystal structure of Escherichia coli MsrB (reduced form)

PDB DOI: https://doi.org/10.2210/pdb6SYM/pdb

Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-09-30 Released: 2020-10-14
Deposition Author(s): Napolitano, S., Zyla, D., Glockshuber, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free:
0.245 (DCC)
R-Value Work:
0.211 (DCC)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

Structure of Peptide methionine sulfoxide reductase MsrB at 1.63 Angstrom resolution

Napolitano, S., Zyla, D., Glockshuber, R.

To be published.

Macromolecule Content

Total Structure Weight: 31.31 kDa
Atom Count: 2,286
Modeled Residue Count: 269
Deposited Residue Count: 274
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide methionine sulfoxide reductase MsrB	A, B	137	Escherichia coli K-12	Mutation(s): 0 Gene Names: msrB, yeaA, b1778, JW1767 EC: 1.8.4.12
UniProt
Find proteins for P0A746 (Escherichia coli (strain K12)) Explore P0A746 Go to UniProtKB: P0A746
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A746
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CAF Query on CAF	A, B	L-PEPTIDE LINKING	C₅ H₁₂ As N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free: 0.245 (DCC)
R-Value Work: 0.211 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.39	α = 90
b = 56.27	β = 90
c = 85.61	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-10-14

Deposition Author(s):

Glockshuber, R.

Revision History (Full details and data files)

Version 1.0: 2020-10-14
Type: Initial release
Version 1.1: 2024-05-01
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-06
Changes: 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.