2UYR | pdb_00002uyr

Crystal structure of Bacillus cereus sphingomyelinase mutant :N57A

PDB DOI: https://doi.org/10.2210/pdb2UYR/pdb

Classification: HYDROLASE
Organism(s): Bacillus cereus
Expression System: Bacillus subtilis
Mutation(s): Yes

Deposited: 2007-04-12 Released: 2008-05-27
Deposition Author(s): Oda, M., Tsuge, H., Sakurai, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.235 (Depositor)
R-Value Work:
0.182 (Depositor), 0.177 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Model: experimental
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This is version 1.5 of the entry. See complete history.

Literature

Crystal Structure of Bacillus Cereus Sphingomyelinase Mutant : N57A

Oda, M., Tsuge, H., Sakurai, J.

To be published.

Macromolecule Content

Total Structure Weight: 34.3 kDa
Atom Count: 2,451
Modeled Residue Count: 299
Deposited Residue Count: 306
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SPHINGOMYELINASE C	A [auth X]	306	Bacillus cereus	Mutation(s): 1 EC: 3.1.4.12
UniProt
Find proteins for P11889 (Bacillus cereus) Explore P11889 Go to UniProtKB: P11889
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11889
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain B [auth X] MOL2 format, chain B [auth X] mmCIF format, chain B [auth X]	B [auth X]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth X] Interactions & Density Focus chain B [auth X]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.235 (Depositor)
R-Value Work: 0.182 (Depositor), 0.177 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.09	α = 90
b = 63.927	β = 90
c = 101.69	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CCP4I	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-05-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-05-27
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2018-04-04
Changes: Data collection
Version 1.4: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description
Version 1.5: 2024-10-16
Changes: 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.