3DKU | pdb_00003dku

Crystal structure of Nudix hydrolase Orf153, ymfB, from Escherichia coli K-1

• PDB DOI: https://doi.org/10.2210/pdb3DKU/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli APEC O1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-06-26 Released: 2009-06-30 
• Deposition Author(s): Hong, M.K., Kim, J.K., Jung, J.H., Jung, J.W., Choi, J.Y., Kang, L.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.69 Å
• R-Value Free: 
  0.270 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Nudix hydrolase Orf153, ymfB, from Escherichia coli K-1.

Hong, M.K., Kim, J.K., Jung, J.H., Jung, J.W., Choi, J.Y., Kang, L.W.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 5  

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

Biological assembly 5 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 6  

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

Biological assembly 6 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 7  

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

Biological assembly 7 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 8  

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

Biological assembly 8 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 139.61 kDa 
• Atom Count: 9,800 
• Modeled Residue Count: 1,201 
• Deposited Residue Count: 1,224 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative phosphohydrolase	A, B, C, D, E, F, G, H	153	Escherichia coli APEC O1	Mutation(s): 0  EC: 3.6.1
UniProt
Find proteins for A1AA28 (Escherichia coli O1:K1 / APEC) Explore A1AA28  Go to UniProtKB:  A1AA28

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.69 Å
• R-Value Free:  0.270 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.96	α = 90
b = 70.521	β = 103.3
c = 145.031	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-30 
Deposition Author(s): Hong, M.K., Kim, J.K., Jung, J.H., Jung, J.W., Choi, J.Y., Kang, L.W.

Revision History  

• Version 1.0: 2009-06-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence
• Version 1.3: 2019-12-25
  Changes: Derived calculations
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Refinement description