Macromolecule Content

Total Structure Weight: 43.51 kDa
Atom Count: 3068
Modelled Residue Count: 378
Deposited Residue Count: 394
Unique protein chains: 1

3OKP

Crystal structure of Corynebacterium glutamicum PimB' bound to GDP-Man (orthorhombic crystal form)

DOI: 10.2210/pdb3OKP/pdb

Classification: TRANSFERASE
Organism(s): Corynebacterium glutamicum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-08-25 Released: 2010-09-15
Deposition Author(s): Batt, S.M., Jabeen, T., Besra, G.S., Futterer, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.232
R-Value Work: 0.203
R-Value Observed: 0.204

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Acceptor substrate discrimination in phosphatidyl-myo-inositol mannoside synthesis: structural and mutational analysis of mannosyltransferase Corynebacterium glutamicum PimB'.

Batt, S.M., Jabeen, T., Mishra, A.K., Veerapen, N., Krumbach, K., Eggeling, L., Besra, G.S., Futterer, K.

(2010) J Biol Chem 285: 37741-37752

PubMed: 20843801 Search on PubMedSearch on PubMed Central
DOI: 10.1074/jbc.M110.165407
Primary Citation of Related Structures:
3OKA, 3OKC, 3OKP

PubMed Abstract:

Macromolecules

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(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GDP-mannose-dependent alpha-(1-6)-phosphatidylinositol monomannoside mannosyltransferase	A	394	Corynebacterium glutamicum	Mutation(s): 0 Gene Names: cg2400, Cgl2186, NCGL2106, pimB EC: 2.4.1.57 (PDB Primary Data), 2.4.1.346 (UniProt)
UniProt
Find proteins for Q8NNK8 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025)) Explore Q8NNK8 Go to UniProtKB: Q8NNK8
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDD (Subject of Investigation/LOI) Query on GDD Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE C₁₆ H₂₅ N₅ O₁₆ P₂ MVMSCBBUIHUTGJ-GDJBGNAASA-N		Ligand Interaction

Binding Affinity Annotations
ID	Source	Binding Affinity
GDD	Binding MOAD: 3OKP	Kd: 1.90e+4 (nM) from 1 assay(s)
GDD	PDBBind: 3OKP	Kd: 1.90e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.232
R-Value Work: 0.203
R-Value Observed: 0.204
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.746	α = 90
b = 87.002	β = 90
c = 106.895	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Deposited Date: 2010-08-25
Released Date: 2010-09-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-09-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance

RCSB PDB is funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.