4Z9N | pdb_00004z9n

ABC transporter / periplasmic binding protein from Brucella ovis with glutathione bound

PDB DOI: https://doi.org/10.2210/pdb4Z9N/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Brucella ovis ATCC 25840
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-04-10 Released: 2015-06-17
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.183 (Depositor), 0.184 (DCC)
R-Value Work:
0.152 (Depositor), 0.153 (DCC)
R-Value Observed:
0.152 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

ABC transporter / periplasmic binding protein from Brucella ovis with glutathione bound

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Macromolecule Content

Total Structure Weight: 218.26 kDa
Atom Count: 16,848
Modeled Residue Count: 1,926
Deposited Residue Count: 1,968
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amino acid ABC transporter, periplasmic amino acid-binding protein	A, B, C, D, E A, B, C, D, E, F	328	Brucella ovis ATCC 25840	Mutation(s): 0 Gene Names: BOV_0736
UniProt
Find proteins for A0A0M3KL33 (Brucella ovis (strain ATCC 25840 / 63/290 / NCTC 10512)) Explore A0A0M3KL33 Go to UniProtKB: A0A0M3KL33
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0M3KL33
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GSH Query on GSH Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain Q [auth C] SDF format, chain W [auth E] SDF format, chain Y [auth F] SDF format, chain U [auth D] SDF format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain W [auth E] MOL2 format, chain Y [auth F] MOL2 format, chain U [auth D] MOL2 format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain W [auth E] mmCIF format, chain Y [auth F] mmCIF format, chain U [auth D] mmCIF format, chain G [auth A]	G [auth A] L [auth B] Q [auth C] U [auth D] W [auth E] G [auth A], L [auth B], Q [auth C], U [auth D], W [auth E], Y [auth F]	Glutathione C₁₀ H₁₇ N₃ O₆ S RWSXRVCMGQZWBV-WDSKDSINSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain W [auth E] Focus chain Y [auth F] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain W [auth E] Focus chain Y [auth F]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain S [auth C] SDF format, chain Z [auth F] SDF format, chain X [auth E] SDF format, chain V [auth D] SDF format, chain O [auth B] SDF format, chain N [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain S [auth C] MOL2 format, chain Z [auth F] MOL2 format, chain X [auth E] MOL2 format, chain V [auth D] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain S [auth C] mmCIF format, chain Z [auth F] mmCIF format, chain X [auth E] mmCIF format, chain V [auth D] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B]	I [auth A] J [auth A] N [auth B] O [auth B] S [auth C] I [auth A], J [auth A], N [auth B], O [auth B], S [auth C], V [auth D], X [auth E], Z [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth C] Focus chain V [auth D] Focus chain X [auth E] Focus chain Z [auth F] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth C] Focus chain V [auth D] Focus chain X [auth E] Focus chain Z [auth F]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain T [auth C] SDF format, chain R [auth C] SDF format, chain P [auth B] SDF format, chain M [auth B] SDF format, chain K [auth A] SDF format, chain H [auth A] MOL2 format, chain T [auth C] MOL2 format, chain R [auth C] MOL2 format, chain P [auth B] MOL2 format, chain M [auth B] MOL2 format, chain K [auth A] MOL2 format, chain H [auth A] mmCIF format, chain T [auth C] mmCIF format, chain R [auth C] mmCIF format, chain P [auth B] mmCIF format, chain M [auth B] mmCIF format, chain K [auth A] mmCIF format, chain H [auth A]	H [auth A] K [auth A] M [auth B] P [auth B] R [auth C] H [auth A], K [auth A], M [auth B], P [auth B], R [auth C], T [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain P [auth B] Focus chain R [auth C] Focus chain T [auth C] Interactions & Density Focus chain H [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain P [auth B] Focus chain R [auth C] Focus chain T [auth C]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002593 (GSH) Query on PRD_002593	G [auth A] L [auth B] Q [auth C] U [auth D] W [auth E] G [auth A], L [auth B], Q [auth C], U [auth D], W [auth E], Y [auth F]	Glutathione	Peptide-like / Oxidation-reduction		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain W [auth E] Focus chain Y [auth F] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain W [auth E] Focus chain Y [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.183 (Depositor), 0.184 (DCC)
R-Value Work: 0.152 (Depositor), 0.153 (DCC)
R-Value Observed: 0.152 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.99	α = 90
b = 76.93	β = 94.07
c = 131.47	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2015-06-17

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2015-06-17
Type: Initial release
Version 1.1: 2025-04-02
Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy, Structure summary