3MMS | pdb_00003mms

Crystal structure of Streptococcus pneumoniae MTA/SAH nucleosidase in complex with 8-aminoadenine

PDB DOI: https://doi.org/10.2210/pdb3MMS/pdb

Classification: HYDROLASE
Organism(s): Streptococcus pneumoniae
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2010-04-20 Released: 2010-05-12
Deposition Author(s): Siu, K.K.W., Lee, J.E., Horvatin-Mrakovcic, C., Howell, P.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.199 (Depositor), 0.212 (DCC)
R-Value Work:
0.182 (Depositor), 0.193 (DCC)

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Ligand Structure Quality Assessment

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

Literature

Crystal structure of Streptococcus pneumoniae MTA/SAH nucleosidase in complex with 8-aminoadenine

Siu, K.K.W., Lee, J.E., Horvatin-Mrakovcic, C., Howell, P.L.

To be published.

Macromolecule Content

Total Structure Weight: 25.04 kDa
Atom Count: 1,967
Modeled Residue Count: 225
Deposited Residue Count: 230
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-methylthioadenosine / S-adenosylhomocysteine nucleosidase	A	230	Streptococcus pneumoniae	Mutation(s): 4 Gene Names: mtnN, pfs, SPP_0997, spr0894 EC: 3.2.2.16 (PDB Primary Data), 3.2.2.9 (UniProt)
UniProt
Find proteins for A0A0H2UPP7 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore A0A0H2UPP7 Go to UniProtKB: A0A0H2UPP7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H2UPP7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Q88 Query on Q88 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	9H-purine-6,8-diamine C₅ H₆ N₆ PFUVOLUPRFCPMN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.199 (Depositor), 0.212 (DCC)
R-Value Work: 0.182 (Depositor), 0.193 (DCC)

Space Group: I 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.72	α = 90
b = 145.72	β = 90
c = 145.72	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
d*TREK	data reduction
CNS	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-05-12

Deposition Author(s):

Horvatin-Mrakovcic, C.

Revision History (Full details and data files)

Version 1.0: 2010-05-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-10-06
Changes: Database references, Derived calculations
Version 1.3: 2024-02-21
Changes: Data collection

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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.