2I2L | pdb_00002i2l

X-ray Crystal Structure of Protein yopX from Bacillus subtilis. Northeast Structural Genomics Consortium Target SR411.

PDB DOI: https://doi.org/10.2210/pdb2I2L/pdb

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

Deposited: 2006-08-16 Released: 2006-08-29
Deposition Author(s): Vorobiev, S.M., Zhou, W., Seetharaman, J., Forouhar, F., Kuzin, A.A., Ho, C.K., Janjua, H., Cunningham, K., Ma, L.C., Xiao, R., Liu, J., Acton, T., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.286 (Depositor), 0.301 (DCC)
R-Value Work:
0.241 (Depositor), 0.253 (DCC)
R-Value Observed:
0.241 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the hypothetical protein yopX from Bacillus subtilis

Vorobiev, S.M., Zhou, W., Seetharaman, J., Forouhar, F., Kuzin, A.A., Ho, C.K., Cunningham, K., Ma, L.C., Xiao, R., Liu, J., Acton, T., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Macromolecule Content

Total Structure Weight: 49.26 kDa
Atom Count: 3,102
Modeled Residue Count: 391
Deposited Residue Count: 426
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YopX protein	A, B, C	142	Bacillus subtilis	Mutation(s): 3 Gene Names: yopX
UniProt
Find proteins for O34401 (Bacillus subtilis (strain 168)) Explore O34401 Go to UniProtKB: O34401
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O34401
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.286 (Depositor), 0.301 (DCC)
R-Value Work: 0.241 (Depositor), 0.253 (DCC)
R-Value Observed: 0.241 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.521	α = 90
b = 99.521	β = 90
c = 87.43	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
SHELXD	phasing
SHELXE	model building
RESOLVE	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2006-08-29

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2006-08-29
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary