2NX2 | pdb_00002nx2

Crystal structure of protein ypsA from Bacillus subtilis, Pfam DUF1273

PDB DOI: https://doi.org/10.2210/pdb2NX2/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Bacillus subtilis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2006-11-16 Released: 2006-12-19
Deposition Author(s): Ramagopal, U.A., Alvarado, J., Dickey, M., Reyes, C., Toro, R., Bain, K., Gheyi, T., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.224 (Depositor), 0.219 (DCC)
R-Value Work:
0.180 (Depositor), 0.179 (DCC)
R-Value Observed:
0.182 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2NX2

This is version 1.6 of the entry. See complete history.

Literature

Crystal structure of hypothetical protein ypsA from Bacillus subtilis.

Ramagopal, U.A., Alvarado, J., Dickey, M., Reyes, C., Toro, R., Bain, K., Gheyi, T., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics

To be published.

Macromolecule Content

Total Structure Weight: 21.15 kDa
Atom Count: 1,648
Modeled Residue Count: 178
Deposited Residue Count: 181
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein ypsA	A	181	Bacillus subtilis	Mutation(s): 0 Gene Names: ypsA
UniProt
Find proteins for P50838 (Bacillus subtilis (strain 168)) Explore P50838 Go to UniProtKB: P50838
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P50838
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.224 (Depositor), 0.219 (DCC)
R-Value Work: 0.180 (Depositor), 0.179 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.052	α = 90
b = 51.052	β = 90
c = 138.22	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing
SHELXE	model building

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2006-12-19

Deposition Author(s):

Ramagopal, U.A.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2006-12-19
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: 2017-10-18
Changes: Refinement description
Version 1.4: 2018-11-14
Changes: Data collection, Structure summary
Version 1.5: 2021-02-03
Changes: Database references, Structure summary
Version 1.6: 2023-12-27
Changes: Data collection, Database references

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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.