6NIO | pdb_00006nio

Crystal Structure of the Molybdate Transporter Periplasmic Protein ModA from Yersinia pestis

• PDB DOI: https://doi.org/10.2210/pdb6NIO/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Yersinia pestis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-12-31 Released: 2019-01-16 
• Deposition Author(s): Kim, Y., Joachimiak, G., Maltseva, N., Endres, M., 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free: 
  0.179 (Depositor), 0.179 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Literature

Crystal Structure of the Molybdate Transporter Periplasmic Protein ModA from Yersinia pestis

Kim, Y., Joachimiak, G., Maltseva, N., Endres, M., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 26.03 kDa 
• Atom Count: 2,067 
• Modeled Residue Count: 231 
• Deposited Residue Count: 235 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Molybdate ABC transporter substrate-binding protein	A	235	Yersinia pestis	Mutation(s): 0  Gene Names: modA, modA2, YP_1015, C6P89_14820, NCTC144_03853

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NHE	B [auth A]	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C8 H17 N O3 S MKWKNSIESPFAQN-UHFFFAOYSA-N
ACY	C [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
FMT	D [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free:  0.179 (Depositor), 0.179 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.922	α = 90
b = 54.305	β = 90
c = 69.785	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-01-16 
Deposition Author(s): Kim, Y., Joachimiak, G., Maltseva, N., Endres, M., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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

Revision History  

• Version 1.0: 2019-01-16
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Structure summary