1NS5 | pdb_00001ns5

X-RAY STRUCTURE OF YBEA FROM E.COLI. NORTHEAST STRUCTURAL GENOMICS RESEARCH CONSORTIUM (NESG) TARGET ER45

PDB DOI: https://doi.org/10.2210/pdb1NS5/pdb

Classification: Structural Genomics, Unknown Function
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2003-01-27 Released: 2003-02-04
Deposition Author(s): Benach, J., Shen, J., Rost, B., Xiao, R., Acton, T., Montelione, G., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.68 Å
R-Value Free:
0.213 (Depositor)
R-Value Work:
0.145 (Depositor), 0.162 (DCC)
R-Value Observed:
0.145 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1NS5

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

Literature

Structure of YBEA from E. coli

BENACH, J., SHEN, J., ROST, B., XIAO, R., ACTON, T., MONTELIONE, G., HUNT, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 35.11 kDa
Atom Count: 2,832
Modeled Residue Count: 308
Deposited Residue Count: 310
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein ybeA	A, B	155	Escherichia coli	Mutation(s): 4 Gene Names: ybea EC: 2.1.1.177
UniProt
Find proteins for P0A8I8 (Escherichia coli (strain K12)) Explore P0A8I8 Go to UniProtKB: P0A8I8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A8I8
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: 1.68 Å
R-Value Free: 0.213 (Depositor)
R-Value Work: 0.145 (Depositor), 0.162 (DCC)
R-Value Observed: 0.145 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.922	α = 90
b = 58.652	β = 102.15
c = 57.415	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2003-02-04

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2003-02-04
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2024-10-09
Changes: Data collection, Database references, 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.