5DW8 | pdb_00005dw8

Crystal structure of 2'AMP bound SaIMPase-II

PDB DOI: https://doi.org/10.2210/pdb5DW8/pdb

Classification: HYDROLASE
Organism(s): Staphylococcus aureus
Expression System: Escherichia coli M15
Mutation(s): No

Deposited: 2015-09-22 Released: 2015-12-09
Deposition Author(s): Dutta, A., Bhattacharyya, S., Das, A.K.
Funding Organization(s): Department of Biotechnology

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.266 (Depositor), 0.269 (DCC)
R-Value Work:
0.205 (Depositor), 0.210 (DCC)
R-Value Observed:
0.209 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

Crystal structure of 2'AMP bound SaIMPase-II

Dutta, A., Bhattacharyya, S., Das, A.K.

To be published.

Macromolecule Content

Total Structure Weight: 63.87 kDa
Atom Count: 4,192
Modeled Residue Count: 519
Deposited Residue Count: 566
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inositol monophosphatase	A, B	283	Staphylococcus aureus	Mutation(s): 0 Gene Names: sas1042 EC: 3.1.3.25

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2AM Query on 2AM Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain I [auth B]	D [auth A], I [auth B]	ADENOSINE-2'-MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P QDFHPFSBQFLLSW-KQYNXXCUSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B]	C [auth A], E [auth A], G [auth B], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.266 (Depositor), 0.269 (DCC)
R-Value Work: 0.205 (Depositor), 0.210 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.008	α = 90
b = 105.687	β = 101.91
c = 53.313	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2015-12-09

Deposition Author(s):

Bhattacharyya, S.

Funding Organization	Location	Grant Number
Department of Biotechnology	India	--

Revision History (Full details and data files)

Version 1.0: 2015-12-09
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references, Derived calculations

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