3SMD | pdb_00003smd

Crystal structure of a mut/nudix family protein from bacillus thuringiensis

PDB DOI: https://doi.org/10.2210/pdb3SMD/pdb
Entry: 3SMD supersedes: 3EDS

Classification: Structural Genomics, Unknown Function
Organism(s): Bacillus thuringiensis str. Al Hakam
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-06-27 Released: 2011-07-20
Deposition Author(s): Palani, K., Kumaran, D., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free:
0.259 (Depositor), 0.270 (DCC)
R-Value Work:
0.227 (Depositor), 0.240 (DCC)
R-Value Observed:
0.227 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a mut/nudix family protein from bacillus thuringiensis

Palani, K., Kumaran, D., Burley, S.K., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 17.59 kDa
Atom Count: 1,208
Modeled Residue Count: 133
Deposited Residue Count: 153
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MutT/NUDIX family protein	A	153	Bacillus thuringiensis str. Al Hakam	Mutation(s): 0 Gene Names: balh_2480
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.259 (Depositor), 0.270 (DCC)
R-Value Work: 0.227 (Depositor), 0.240 (DCC)
R-Value Observed: 0.227 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64	α = 90
b = 64	β = 90
c = 59.01	γ = 120

Software Package:

Software Name	Purpose
CBASS	data collection
SHELXD	phasing
SHARP	phasing
ARP/wARP	model building
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-07-20

Deposition Author(s):

Swaminathan, S.

New York SGX Research Center for Structural Genomics (NYSGXRC)

This entry supersedes: 3EDS

Revision History (Full details and data files)

Version 1.0: 2011-07-20
Type: Initial release
Version 1.1: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.2: 2024-10-16
Changes: Data collection, Database references, Structure summary

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.