3E7N

Crystal structure of d-ribose high-affinity transport system from salmonella typhimurium lt2

PDB DOI: https://doi.org/10.2210/pdb3E7N/pdb
Entry: 3E7N supersedes: 3DSA

Classification: TRANSPORT PROTEIN
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-08-18 Released: 2008-08-26
Deposition Author(s): Nocek, B., Maltseva, N., Gu, M., Joachimiak, A., Anderson, W., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.233
R-Value Work: 0.191
R-Value Observed: 0.193

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of d-ribose high-affinity transport system from salmonella typhimurium lt2

Nocek, B., Maltseva, N., Gu, M., Joachimiak, A., Anderson, W., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 235.77 kDa
Atom Count: 16,381
Modelled Residue Count: 2,101
Deposited Residue Count: 2,130
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-ribose high-affinity transport system	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O	142	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0 Gene Names: rbsD, STM3881
UniProt
Find proteins for Q8ZKW0 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZKW0 Go to UniProtKB: Q8ZKW0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8ZKW0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth N] SDF format, chain P [auth A] SDF format, chain S [auth D] SDF format, chain W [auth H] SDF format, chain BA [auth O] SDF format, chain Q [auth B] SDF format, chain R [auth C] SDF format, chain T [auth E] SDF format, chain U [auth F] SDF format, chain V [auth G] SDF format, chain X [auth J] SDF format, chain Y [auth K] SDF format, chain Z [auth L] MOL2 format, chain AA [auth N] MOL2 format, chain P [auth A] MOL2 format, chain S [auth D] MOL2 format, chain W [auth H] MOL2 format, chain BA [auth O] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth C] MOL2 format, chain T [auth E] MOL2 format, chain U [auth F] MOL2 format, chain V [auth G] MOL2 format, chain X [auth J] MOL2 format, chain Y [auth K] MOL2 format, chain Z [auth L] mmCIF format, chain AA [auth N] mmCIF format, chain P [auth A] mmCIF format, chain S [auth D] mmCIF format, chain W [auth H] mmCIF format, chain BA [auth O] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth C] mmCIF format, chain T [auth E] mmCIF format, chain U [auth F] mmCIF format, chain V [auth G] mmCIF format, chain X [auth J] mmCIF format, chain Y [auth K] mmCIF format, chain Z [auth L]	AA [auth N] BA [auth O] P [auth A] Q [auth B] R [auth C] AA [auth N], BA [auth O], P [auth A], Q [auth B], R [auth C], S [auth D], T [auth E], U [auth F], V [auth G], W [auth H], X [auth J], Y [auth K], Z [auth L]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth N] Focus chain BA [auth O] Focus chain P [auth A] Focus chain Q [auth B] Focus chain R [auth C] Focus chain S [auth D] Focus chain T [auth E] Focus chain U [auth F] Focus chain V [auth G] Focus chain W [auth H] Focus chain X [auth J] Focus chain Y [auth K] Focus chain Z [auth L] Interactions & Density Focus chain AA [auth N] Focus chain BA [auth O] Focus chain P [auth A] Focus chain Q [auth B] Focus chain R [auth C] Focus chain S [auth D] Focus chain T [auth E] Focus chain U [auth F] Focus chain V [auth G] Focus chain W [auth H] Focus chain X [auth J] Focus chain Y [auth K] Focus chain Z [auth L]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.233
R-Value Work: 0.191
R-Value Observed: 0.193
Space Group: C 1 2 1
Diffraction Data: https://doi.org/10.18430/m33e7n

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 293.042	α = 90
b = 92.726	β = 106.53
c = 93.601	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELX	phasing
Coot	model building
MLPHARE	phasing
CCP4	phasing
PHENIX	phasing