6FMG | pdb_00006fmg

Structure of the Mannose Transporter IIA Domain from Streptococcus pneumoniae

PDB DOI: https://doi.org/10.2210/pdb6FMG/pdb

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

Deposited: 2018-01-31 Released: 2019-03-13
Deposition Author(s): Magoch, M., Grudnik, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.197 (Depositor), 0.200 (DCC)
R-Value Work:
0.170 (Depositor), 0.170 (DCC)
R-Value Observed:
0.172 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structure of the Mannose Transporter IIA Domain from Streptococcus pneumoniae

Magoch, M., Grudnik, P., Nogly, P., Dubin, G., Archer, M., Ma, P.

To be published.

Macromolecule Content

Total Structure Weight: 60.19 kDa
Atom Count: 4,662
Modeled Residue Count: 560
Deposited Residue Count: 560
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PTS system mannose-specific transporter subunit IIAB	A, B, C, D	140	Streptococcus pneumoniae	Mutation(s): 0 Gene Names: manL_2, ERS020456_01132 EC: 2.7.1.69
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.197 (Depositor), 0.200 (DCC)
R-Value Work: 0.170 (Depositor), 0.170 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.528	α = 90
b = 138.528	β = 90
c = 69.767	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
PHASER	phasing
Coot	model building

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-03-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-03-13
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, 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.