7L8N | pdb_00007l8n

Diadenylate cyclase with AMP from Streptococcus mutans

PDB DOI: https://doi.org/10.2210/pdb7L8N/pdb

Classification: TRANSFERASE
Organism(s): Streptococcus mutans UA159
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2020-12-31 Released: 2022-01-19
Deposition Author(s): Hua, Z., Hui, W.
Funding Organization(s): National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free:
0.207 (Depositor), 0.206 (DCC)
R-Value Work:
0.161 (Depositor), 0.161 (DCC)
R-Value Observed:
0.164 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Diadenylate cyclase with AMP from Streptococcus mutans

Hua, Z., Hui, W.

To be published.

Macromolecule Content

Total Structure Weight: 33.46 kDa
Atom Count: 2,539
Modeled Residue Count: 301
Deposited Residue Count: 302
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diadenylate cyclase	A, B	151	Streptococcus mutans UA159	Mutation(s): 0 Gene Names: dacA, SMU_1428c EC: 2.7.7.85
UniProt
Find proteins for Q8DTC4 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159)) Explore Q8DTC4 Go to UniProtKB: Q8DTC4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8DTC4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP (Subject of Investigation/LOI) Query on AMP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MLI Query on MLI Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B]	G [auth B], H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain G [auth B] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.207 (Depositor), 0.206 (DCC)
R-Value Work: 0.161 (Depositor), 0.161 (DCC)
R-Value Observed: 0.164 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.36	α = 90
b = 84.59	β = 90
c = 100.24	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-01-19

Deposition Author(s):

Hua, Z.

Hui, W.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)	United States	R01DE028329
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)	United States	R01DE022350