1YLM | pdb_00001ylm

Structure of Cytosolic Protein of Unknown Function YutE from Bacillus subtilis

PDB DOI: https://doi.org/10.2210/pdb1YLM/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Bacillus subtilis subsp. subtilis str. 168
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2005-01-19 Released: 2005-03-01
Deposition Author(s): Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free:
0.238 (Depositor), 0.238 (DCC)
R-Value Work:
0.200 (Depositor), 0.199 (DCC)
R-Value Observed:
0.202 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1YLM

This is version 1.3 of the entry. See complete history.

Literature

Hypothetical cytosolic protein YutE from Bacillus subtilis

Binkowski, T.A., Quartey, P., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 33.72 kDa
Atom Count: 2,659
Modeled Residue Count: 286
Deposited Residue Count: 288
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein BSU32300	A, B	144	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 4 Gene Names: YutE EC: 3.1
UniProt
Find proteins for O32126 (Bacillus subtilis (strain 168)) Explore O32126 Go to UniProtKB: O32126
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O32126
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free: 0.238 (Depositor), 0.238 (DCC)
R-Value Work: 0.200 (Depositor), 0.199 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.914	α = 90
b = 72.081	β = 115.24
c = 76.552	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2005-03-01

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2005-03-01
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-11-13
Changes: Data collection, Database references, Derived calculations, 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.