3QFM | pdb_00003qfm

Crystal structure of Streptococcal asymmetric Ap4A hydrolase and phosphodiesterase Spr1479/SapH

PDB DOI: https://doi.org/10.2210/pdb3QFM/pdb

Classification: HYDROLASE
Organism(s): Streptococcus pneumoniae R6
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-01-22 Released: 2011-08-24
Deposition Author(s): Jiang, Y.L., Zhang, J.W., Yu, W.L., Cheng, W., Zhang, C.C., Zhou, C.Z., Chen, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.229 (Depositor), 0.228 (DCC)
R-Value Work:
0.195 (Depositor), 0.194 (DCC)
R-Value Observed:
0.196 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3QFM

This is version 1.1 of the entry. See complete history.

Literature

Structural and enzymatic characterization of a Streptococcal ATP/diadenosine polyphosphate and phosphodiester hydrolase Spr1479/SapH

Jiang, Y.L., Zhang, J.W., Yu, W.L., Cheng, W., Zhang, C.C., Frolet, C., Di-guilmi, A.-M., Vernet, T., Zhou, C.Z., Chen, Y.

To be published.

Macromolecule Content

Total Structure Weight: 63.07 kDa
Atom Count: 4,428
Modeled Residue Count: 508
Deposited Residue Count: 540
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	A, B	270	Streptococcus pneumoniae R6	Mutation(s): 0 Gene Names: spr1479
UniProt
Find proteins for Q8DNX4 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6)) Explore Q8DNX4 Go to UniProtKB: Q8DNX4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8DNX4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.229 (Depositor), 0.228 (DCC)
R-Value Work: 0.195 (Depositor), 0.194 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.559	α = 90
b = 75.102	β = 90
c = 148.796	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
SOLVE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-08-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-08-24
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references, Derived calculations

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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.