2IM8

X-Ray Crystal Structure of Protein yppE from Bacillus subtilis. Northeast Structural Genomics Consortium Target SR213.

PDB DOI: https://doi.org/10.2210/pdb2IM8/pdb

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

Deposited: 2006-10-03 Released: 2006-10-17
Deposition Author(s): Kuzin, A.P., Shastry, R., Janjua, H., Cunningham, K., Ma, L.C., Xiao, R., Liu, J., Hang, D., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.257
R-Value Work: 0.236
R-Value Observed: 0.236

wwPDB Validation 3D Report Full Report

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

Literature

X-Ray structure of hypothetical protein yPPE. Northeast Structural Genomics Consortium target SR213.

Kuzin, A.P., Neely, H., Seetharaman, J., Shastry, R., Janjua, H., Cunningham, K., Ma, L.C., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 31.49 kDa
Atom Count: 2,144
Modelled Residue Count: 239
Deposited Residue Count: 262
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein yppE	A, B	131	Bacillus subtilis	Mutation(s): 3 Gene Names: yppE
UniProt
Find proteins for P50833 (Bacillus subtilis (strain 168)) Explore P50833 Go to UniProtKB: P50833
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P50833
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

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: 2.00 Å
R-Value Free: 0.257
R-Value Work: 0.236
R-Value Observed: 0.236
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.735	α = 90
b = 70.83	β = 90
c = 76.237	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2006-10-17

Deposition Author(s):

Montelione, G.T.

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2006-10-17
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.