3ROT | pdb_00003rot

Crystal structure of ABC sugar transporter (periplasmic sugar binding protein) from Legionella pneumophila

PDB DOI: https://doi.org/10.2210/pdb3ROT/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-04-26 Released: 2011-05-18
Deposition Author(s): Eswaramoorthy, S., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free:
0.254 (Depositor), 0.256 (DCC)
R-Value Work:
0.220 (Depositor), 0.221 (DCC)
R-Value Observed:
0.220 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of ABC sugar transporter (periplasmic sugar binding protein) from Legionella pneumophila

Eswaramoorthy, S., Almo, S.C., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 68.24 kDa
Atom Count: 4,411
Modeled Residue Count: 545
Deposited Residue Count: 594
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC sugar transporter, periplasmic sugar binding protein	A, B	297	Legionella pneumophila subsp. pneumophila str. Philadelphia 1	Mutation(s): 0 Gene Names: lpg0184
UniProt
Find proteins for Q5ZZ27 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZZ27 Go to UniProtKB: Q5ZZ27
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5ZZ27
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free: 0.254 (Depositor), 0.256 (DCC)
R-Value Work: 0.220 (Depositor), 0.221 (DCC)
R-Value Observed: 0.220 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.693	α = 90
b = 117.86	β = 107.39
c = 54.607	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELX	model building
SHARP	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-05-18

Deposition Author(s):

Eswaramoorthy, S.

Swaminathan, S.

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2011-05-18
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.