3RPE | pdb_00003rpe

1.1 Angstrom Crystal Structure of Putative Modulator of Drug Activity (MdaB) from Yersinia pestis CO92.

• PDB DOI: https://doi.org/10.2210/pdb3RPE/pdb

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


• Deposited: 2011-04-26 Released: 2011-05-04 
• Deposition Author(s): Minasov, G., Halavaty, A., Shuvalova, L., Dubrovska, I., Winsor, J., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 
  0.117 (Depositor), 0.121 (DCC) 
• R-Value Work: 
  0.100 (Depositor), 0.104 (DCC) 
• R-Value Observed: 
  0.100 (Depositor) 

Starting Model: experimental

Literature

1.1 Angstrom Crystal Structure of Putative Modulator of Drug Activity (MdaB) from Yersinia pestis CO92.

Minasov, G., Halavaty, A., Shuvalova, L., Dubrovska, I., Winsor, J., Papazisi, L., 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: 51.18 kDa 
• Atom Count: 4,047 
• Modeled Residue Count: 392 
• Deposited Residue Count: 436 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Modulator of drug activity B	A, B	218	Yersinia pestis	Mutation(s): 0  Gene Names: mda66, mdaB, mdaB3, y3509, YPO0670, YP_2985 EC: 1.6.5.10
UniProt
Find proteins for A0A0H2W7Q5 (Yersinia pestis) Explore A0A0H2W7Q5  Go to UniProtKB:  A0A0H2W7Q5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A], E [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
PEG	D [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free:  0.117 (Depositor), 0.121 (DCC) 
• R-Value Work:  0.100 (Depositor), 0.104 (DCC) 
• R-Value Observed: 0.100 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33rpe

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.497	α = 90
b = 66.497	β = 90
c = 76.208	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-04 
Deposition Author(s): Minasov, G., Halavaty, A., Shuvalova, L., Dubrovska, I., Winsor, J., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2011-05-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description