5V4A | pdb_00005v4a

A New Glycosyltransferase (DUF1792) from Streptococcus sanguinis

PDB DOI: https://doi.org/10.2210/pdb5V4A/pdb

Classification: TRANSFERASE
Organism(s): Streptococcus sanguinis SK36
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-03-08 Released: 2017-09-13
Deposition Author(s): Zhang, H., Wu, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.269 (Depositor), 0.270 (DCC)
R-Value Work:
0.206 (Depositor), 0.210 (DCC)
R-Value Observed:
0.209 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

A New Glycosyltransferase (DUF1792) from Streptococcus sanguinis

Zhang, H., Wu, H.

To be published.

Macromolecule Content

Total Structure Weight: 63.77 kDa
Atom Count: 5,015
Modeled Residue Count: 536
Deposited Residue Count: 548
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLYCOSYLTRANSFERASE (DUF1792)	A, B	274	Streptococcus sanguinis SK36	Mutation(s): 0 Gene Names: SSA_0830
UniProt
Find proteins for A3CM53 (Streptococcus sanguinis (strain SK36)) Explore A3CM53 Go to UniProtKB: A3CM53
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A3CM53
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UDP Query on UDP Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.269 (Depositor), 0.270 (DCC)
R-Value Work: 0.206 (Depositor), 0.210 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.65	α = 90
b = 99.86	β = 90
c = 140.12	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-09-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-09-13
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 1.2: 2024-03-06
Changes: Data collection, Database references

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.