2IIB | pdb_00002iib

Crystal structure of Pasteurella multocida sialyltransferase D141N mutant with CMP bound

PDB DOI: https://doi.org/10.2210/pdb2IIB/pdb

Classification: TRANSFERASE
Organism(s): Pasteurella multocida
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2006-09-27 Released: 2007-08-14
Deposition Author(s): Ni, L., Fisher, A.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.239 (Depositor), 0.230 (DCC)
R-Value Work:
0.197 (Depositor), 0.190 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structural analysis of multifunctional sialyltransferase from Pasteurella multocida.

Ni, L., Huang, S., Yu, H., Cao, H., Sun, M., Chen, X., Fisher, A.J.

To be published.

Macromolecule Content

Total Structure Weight: 46.79 kDa
Atom Count: 3,467
Modeled Residue Count: 377
Deposited Residue Count: 399
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-2,3/2,6-sialyltransferase/sialidase	A	399	Pasteurella multocida	Mutation(s): 1 Gene Names: Pm0188 EC: 2.4.99.4
UniProt
Find proteins for Q15KI8 (Pasteurella multocida) Explore Q15KI8 Go to UniProtKB: Q15KI8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q15KI8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
C5P Query on C5P Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CYTIDINE-5'-MONOPHOSPHATE C₉ H₁₄ N₃ O₈ P IERHLVCPSMICTF-XVFCMESISA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.239 (Depositor), 0.230 (DCC)
R-Value Work: 0.197 (Depositor), 0.190 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.961	α = 90
b = 64.533	β = 98.85
c = 64.251	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PROTEUM PLUS	data collection
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-08-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-08-14
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2021-10-20
Changes: Database references, Derived calculations
Version 1.3: 2023-08-30
Changes: Data collection, Refinement description

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.