3O8S | pdb_00003o8s

Crystal structure of an ADP-ribose pyrophosphatase (SSU98_1448) from STREPTOCOCCUS SUIS 89-1591 at 2.27 A resolution

PDB DOI: https://doi.org/10.2210/pdb3O8S/pdb

Classification: HYDROLASE
Organism(s): Streptococcus suis 89/1591
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-08-03 Released: 2010-08-25
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free:
0.218 (Depositor), 0.225 (DCC)
R-Value Work:
0.191 (Depositor), 0.192 (DCC)
R-Value Observed:
0.193 (Depositor)

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This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of an ADP-ribose pyrophosphatase (SSU98_1448) from STREPTOCOCCUS SUIS 89-1591 at 2.27 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 23.74 kDa
Atom Count: 1,107
Modeled Residue Count: 134
Deposited Residue Count: 206
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribose pyrophosphatase	A	206	Streptococcus suis 89/1591	Mutation(s): 0 Gene Names: SsuiDRAFT_3457

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

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: 2.27 Å
R-Value Free: 0.218 (Depositor), 0.225 (DCC)
R-Value Work: 0.191 (Depositor), 0.192 (DCC)
R-Value Observed: 0.193 (Depositor)

Diffraction Data:

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.78	α = 90
b = 64.78	β = 90
c = 108.29	γ = 90

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement
XSCALE	data processing
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
Rosetta	phasing
PHASER	phasing
BUSTER	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-08-25

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2010-08-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2011-07-20
Changes: Structure summary
Version 1.3: 2023-02-01
Changes: Database references, Derived calculations
Version 1.4: 2024-05-22
Changes: Data collection
Version 1.5: 2024-10-30
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.