9D5W | pdb_00009d5w

Crystal Structure of the Substrate Binding Domain Protein of the ABC Transporter PBP2_YxeM from Vibrio cholerae

PDB DOI: https://doi.org/10.2210/pdb9D5W/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-08-14 Released: 2024-08-28
Deposition Author(s): Kim, Y., Maltseva, N., Grimshaw, S., Joachimiak, A., Center for Structural Biology of Infectious Diseases (CSBID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.229 (Depositor), 0.227 (DCC)
R-Value Work:
0.194 (Depositor), 0.193 (DCC)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

Crystal Structure of the Substrate Binding Domain Protein of the ABC Transporter PBP2_YxeM from Vibrio cholerae

Kim, Y., Maltseva, N., Grimshaw, S., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 232.84 kDa
Atom Count: 16,666
Modeled Residue Count: 2,043
Deposited Residue Count: 2,097
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amino acid ABC transporter, periplasmic amino acid-binding portion	A, B, C, D, E A, B, C, D, E, F, G, H, I	233	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0 Gene Names: VC_0010
UniProt
Find proteins for Q9KVX8 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KVX8 Go to UniProtKB: Q9KVX8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KVX8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain JA [auth G] SDF format, chain KA [auth G] MOL2 format, chain AA [auth D] MOL2 format, chain JA [auth G] MOL2 format, chain KA [auth G] mmCIF format, chain AA [auth D] mmCIF format, chain JA [auth G] mmCIF format, chain KA [auth G]	AA [auth D], JA [auth G], KA [auth G]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth D] Focus chain JA [auth G] Focus chain KA [auth G] Interactions & Density Focus chain AA [auth D] Focus chain JA [auth G] Focus chain KA [auth G]
PGR Query on PGR Download:Ideal Coordinates CCD File SDF format, chain T [auth C] MOL2 format, chain T [auth C] mmCIF format, chain T [auth C]	T [auth C]	R-1,2-PROPANEDIOL C₃ H₈ O₂ DNIAPMSPPWPWGF-GSVOUGTGSA-N		Interactions Focus chain T [auth C] Interactions & Density Focus chain T [auth C]
PGO Query on PGO Download:Ideal Coordinates CCD File SDF format, chain IA [auth G] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain QA [auth I] SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain IA [auth G] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain QA [auth I] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain IA [auth G] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain QA [auth I] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D]	IA [auth G] J [auth A] K [auth A] O [auth B] P [auth B] IA [auth G], J [auth A], K [auth A], O [auth B], P [auth B], QA [auth I], X [auth D], Y [auth D], Z [auth D]	S-1,2-PROPANEDIOL C₃ H₈ O₂ DNIAPMSPPWPWGF-VKHMYHEASA-N		Interactions Focus chain IA [auth G] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain QA [auth I] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain IA [auth G] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain QA [auth I] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain DA [auth E] SDF format, chain N [auth A] SDF format, chain NA [auth G] SDF format, chain S [auth B] SDF format, chain W [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain DA [auth E] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth G] MOL2 format, chain S [auth B] MOL2 format, chain W [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain DA [auth E] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth G] mmCIF format, chain S [auth B] mmCIF format, chain W [auth C]	BA [auth D] DA [auth E] N [auth A] NA [auth G] S [auth B] BA [auth D], DA [auth E], N [auth A], NA [auth G], S [auth B], W [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain DA [auth E] Focus chain N [auth A] Focus chain NA [auth G] Focus chain S [auth B] Focus chain W [auth C] Interactions & Density Focus chain BA [auth D] Focus chain DA [auth E] Focus chain N [auth A] Focus chain NA [auth G] Focus chain S [auth B] Focus chain W [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain EA [auth F] SDF format, chain FA [auth F] SDF format, chain GA [auth F] SDF format, chain L [auth A] SDF format, chain LA [auth G] SDF format, chain OA [auth H] SDF format, chain PA [auth H] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain RA [auth I] SDF format, chain SA [auth I] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain MA [auth G] SDF format, chain M [auth A] SDF format, chain HA [auth F] MOL2 format, chain CA [auth E] MOL2 format, chain EA [auth F] MOL2 format, chain FA [auth F] MOL2 format, chain GA [auth F] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth G] MOL2 format, chain OA [auth H] MOL2 format, chain PA [auth H] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth I] MOL2 format, chain SA [auth I] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain MA [auth G] MOL2 format, chain M [auth A] MOL2 format, chain HA [auth F] mmCIF format, chain CA [auth E] mmCIF format, chain EA [auth F] mmCIF format, chain FA [auth F] mmCIF format, chain GA [auth F] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth G] mmCIF format, chain OA [auth H] mmCIF format, chain PA [auth H] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth I] mmCIF format, chain SA [auth I] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain MA [auth G] mmCIF format, chain M [auth A] mmCIF format, chain HA [auth F]	CA [auth E] EA [auth F] FA [auth F] GA [auth F] HA [auth F] CA [auth E], EA [auth F], FA [auth F], GA [auth F], HA [auth F], L [auth A], LA [auth G], M [auth A], MA [auth G], OA [auth H], PA [auth H], Q [auth B], R [auth B], RA [auth I], SA [auth I], U [auth C], V [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain CA [auth E] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain L [auth A] Focus chain LA [auth G] Focus chain M [auth A] Focus chain MA [auth G] Focus chain OA [auth H] Focus chain PA [auth H] Focus chain Q [auth B] Focus chain R [auth B] Focus chain RA [auth I] Focus chain SA [auth I] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain CA [auth E] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain L [auth A] Focus chain LA [auth G] Focus chain M [auth A] Focus chain MA [auth G] Focus chain OA [auth H] Focus chain PA [auth H] Focus chain Q [auth B] Focus chain R [auth B] Focus chain RA [auth I] Focus chain SA [auth I] Focus chain U [auth C] Focus chain V [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.229 (Depositor), 0.227 (DCC)
R-Value Work: 0.194 (Depositor), 0.193 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.044	α = 90
b = 105.816	β = 119.922
c = 118.124	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
HKL-3000	phasing
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-08-28

Deposition Author(s):

Center for Structural Biology of Infectious Diseases (CSBID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History (Full details and data files)

Version 1.0: 2024-08-28
Type: Initial release

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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.