4S24 | pdb_00004s24

1.7 Angstrom Crystal Structure of of Putative Modulator of Drug Activity (apo- form) from Yersinia pestis CO92

• PDB DOI: https://doi.org/10.2210/pdb4S24/pdb

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


• Deposited: 2015-01-19 Released: 2015-02-04 
• Deposition Author(s): Minasov, G., Shuvalova, L., Dubrovska, I., Flores, K., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.166 (Depositor), 0.165 (DCC) 
• R-Value Work: 
  0.149 (Depositor), 0.148 (DCC) 
• R-Value Observed: 
  0.149 (Depositor) 

Literature

1.7 Angstrom Crystal Structure of of Putative Modulator of Drug Activity (apo- form) from Yersinia pestis CO92.

Minasov, G., Shuvalova, L., Dubrovska, I., Flores, K., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 23.31 kDa 
• Atom Count: 1,897 
• Modeled Residue Count: 192 
• Deposited Residue Count: 197 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Modulator of drug activity B	A	197	Yersinia pestis CO92	Mutation(s): 0  Gene Names: mdaB EC: 1.6.5.10
UniProt
Find proteins for A0A0H2W7Q5 (Yersinia pestis) Explore A0A0H2W7Q5  Go to UniProtKB:  A0A0H2W7Q5

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	F [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
PGE	C [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	D [auth A], E [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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: 1.70 Å
• R-Value Free:  0.166 (Depositor), 0.165 (DCC) 
• R-Value Work:  0.149 (Depositor), 0.148 (DCC) 
• R-Value Observed: 0.149 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34s24

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.046	α = 90
b = 72.046	β = 90
c = 166.766	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
SHELXS	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-02-04 
Deposition Author(s): Minasov, G., Shuvalova, L., Dubrovska, I., Flores, K., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2015-02-04
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary