5KWS | pdb_00005kws

Crystal Structure of Galactose Binding Protein from Yersinia pestis in the Complex with beta D Glucose

• PDB DOI: https://doi.org/10.2210/pdb5KWS/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Yersinia pestis CO92
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-07-19 Released: 2016-08-03 
• Deposition Author(s): Kim, Y., Maltseva, N., Mulligan, R., Grimshaw, 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.32 Å
• R-Value Free: 
  0.160 (Depositor), 0.162 (DCC) 
• R-Value Work: 
  0.144 (Depositor), 0.146 (DCC) 
• R-Value Observed: 
  0.145 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Galactose Binding Protein from Yersinia pestis in the Complex with beta D Glucose

Kim, Y., Maltseva, N., Mulligan, R., Grimshaw, S., Anderson, W.F., 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: 34.6 kDa 
• Atom Count: 2,824 
• Modeled Residue Count: 307 
• Deposited Residue Count: 313 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galactose-binding protein	A	313	Yersinia pestis CO92	Mutation(s): 0  Gene Names: mglB, y2662, YP_1397
UniProt
Find proteins for Q8D072 (Yersinia pestis) Explore Q8D072  Go to UniProtKB:  Q8D072

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BGC	B [auth A]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
GOL	D [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACY	E [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.32 Å
• R-Value Free:  0.160 (Depositor), 0.162 (DCC) 
• R-Value Work:  0.144 (Depositor), 0.146 (DCC) 
• R-Value Observed: 0.145 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m35kws

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.236	α = 90
b = 56.753	β = 90
c = 69.129	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-08-03 
Deposition Author(s): Kim, Y., Maltseva, N., Mulligan, R., Grimshaw, S., Anderson, W.F., 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: 2016-08-03
  Type: Initial release
  
• Version 1.1: 2017-02-08
  Changes: Database references, Structure summary
• Version 1.2: 2017-08-23
  Changes: Data collection
• Version 1.3: 2019-12-04
  Changes: Author supporting evidence, Data collection
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.5: 2023-10-04
  Changes: Data collection, Database references, Refinement description, Structure summary