3L86

The Crystal Structure of smu.665 from Streptococcus mutans UA159

PDB DOI: https://doi.org/10.2210/pdb3L86/pdb

Classification: TRANSFERASE
Organism(s): Streptococcus mutans UA159
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-12-30 Released: 2011-01-05
Deposition Author(s): Su, X.-D., Liu, X., Wu, C.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Free: 0.267
R-Value Work: 0.213
R-Value Observed: 0.216

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

The Crystal Structure of smu.665 from Streptococcus mutans UA159

Su, X.-D., Liu, X., Wu, C.W.

To be published.

Macromolecule Content

Total Structure Weight: 30.54 kDa
Atom Count: 1,919
Modelled Residue Count: 245
Deposited Residue Count: 279
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetylglutamate kinase	A	279	Streptococcus mutans UA159	Mutation(s): 0 Gene Names: smu.665 EC: 2.7.2.8
UniProt
Find proteins for Q8DV44 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159)) Explore Q8DV44 Go to UniProtKB: Q8DV44
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8DV44
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
NLG Query on NLG Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	N-ACETYL-L-GLUTAMATE C₇ H₁₁ N O₅ RFMMMVDNIPUKGG-YFKPBYRVSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-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: 2.06 Å
R-Value Free: 0.267
R-Value Work: 0.213
R-Value Observed: 0.216
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.19	α = 90
b = 94.76	β = 90
c = 47.58	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-01-05

Deposition Author(s):

Su, X.-D.

Liu, X.

Wu, C.W.

Revision History (Full details and data files)

Version 1.0: 2011-01-05
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

3L86

The Crystal Structure of smu.665 from Streptococcus mutans UA159

The Crystal Structure of smu.665 from Streptococcus mutans UA159

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)