5F1Q | pdb_00005f1q

Crystal Structure of Periplasmic Dipeptide Transport Protein from Yersinia pestis

PDB DOI: https://doi.org/10.2210/pdb5F1Q/pdb

Classification: HYDROLASE
Organism(s): Yersinia pestis Nepal516
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-11-30 Released: 2015-12-23
Deposition Author(s): Kim, Y., Zhou, M., Shatsman, S., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free:
0.200 (Depositor), 0.201 (DCC)
R-Value Work:
0.166 (Depositor), 0.168 (DCC)
R-Value Observed:
0.167 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of Periplasmic Dipeptide Transport Protein from Yersinia pestis

Kim, Y., Zhou, M., Shatsman, S., Anderson, W.F., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 125.9 kDa
Atom Count: 8,856
Modeled Residue Count: 1,020
Deposited Residue Count: 1,086
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic dipeptide transport protein	A, B	543	Yersinia pestis Nepal516	Mutation(s): 0 Gene Names: YPN_3652
UniProt
Find proteins for A0A0H2YM47 (Yersinia pestis bv. Antiqua (strain Nepal516)) Explore A0A0H2YM47 Go to UniProtKB: A0A0H2YM47
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H2YM47
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GLN Query on GLN Download:Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A]	J [auth A], K [auth A], R [auth B], S [auth B]	GLUTAMINE C₅ H₁₀ N₂ O₃ ZDXPYRJPNDTMRX-VKHMYHEASA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain R [auth B] Focus chain S [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth A] SDF format, chain I [auth A] SDF format, chain G [auth A] SDF format, chain E [auth A] SDF format, chain C [auth A] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth A] MOL2 format, chain I [auth A] MOL2 format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain C [auth A] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth A] mmCIF format, chain I [auth A] mmCIF format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain C [auth A]	C [auth A] E [auth A] G [auth A] I [auth A] L [auth A] C [auth A], E [auth A], G [auth A], I [auth A], L [auth A], M [auth B], N [auth B], P [auth B], Q [auth B], T [auth B], U [auth B], V [auth B], W [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain L [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain L [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain H [auth A] MOL2 format, chain O [auth B] MOL2 format, chain H [auth A] mmCIF format, chain O [auth B] mmCIF format, chain H [auth A]	H [auth A], O [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain O [auth B] Interactions & Density Focus chain H [auth A] Focus chain O [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: 1.96 Å
R-Value Free: 0.200 (Depositor), 0.201 (DCC)
R-Value Work: 0.166 (Depositor), 0.168 (DCC)
R-Value Observed: 0.167 (Depositor)

Diffraction Data:

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 289.29	α = 90
b = 59.745	β = 103.96
c = 80.631	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
HKL-3000	phasing
SBC-Collect	data collection

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2015-12-23

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

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: 2015-12-23
Type: Initial release
Version 1.1: 2019-11-27
Changes: Author supporting evidence, Derived calculations
Version 1.2: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary