4OEN | pdb_00004oen

Crystal structure of the second substrate binding domain of a putative amino acid ABC transporter from Streptococcus pneumoniae Canada MDR_19A

PDB DOI: https://doi.org/10.2210/pdb4OEN/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Streptococcus pneumoniae str. Canada MDR_19A
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-01-13 Released: 2014-01-22
Deposition Author(s): Stogios, P.J., Wawrzak, Z., Kudritska, M., Yim, V., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.196 (Depositor), 0.217 (DCC)
R-Value Work:
0.161 (Depositor)
R-Value Observed:
0.163 (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

Crystal structure of the second substrate binding domain of a putative amino acid ABC transporter from Streptococcus pneumoniae Canada MDR_19A

Stogios, P.J., Wawrzak, Z., Kudritska, M., Yim, V., Savchenko, A., Anderson, W.F.

To be published.

Macromolecule Content

Total Structure Weight: 48.62 kDa
Atom Count: 4,254
Modeled Residue Count: 442
Deposited Residue Count: 446
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Second substrate binding domain of putative amino acid ABC transporter	A, B	223	Streptococcus pneumoniae str. Canada MDR_19A	Mutation(s): 0 Gene Names: SpneCM_010100001889
UniProt
Find proteins for A0A0H2UQ91 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore A0A0H2UQ91 Go to UniProtKB: A0A0H2UQ91
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H2UQ91
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain C [auth A] MOL2 format, chain J [auth B] MOL2 format, chain C [auth A] mmCIF format, chain J [auth B] mmCIF format, chain C [auth A]	C [auth A], J [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth A] P [auth B] Q [auth B] G [auth A], H [auth A], I [auth A], P [auth B], Q [auth B], R [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] K [auth B] L [auth B] D [auth A], E [auth A], F [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.196 (Depositor), 0.217 (DCC)
R-Value Work: 0.161 (Depositor)
R-Value Observed: 0.163 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.432	α = 90
b = 109.606	β = 111.11
c = 57.922	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
BALBES	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-01-22

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2014-01-22
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description