5C59 | pdb_00005c59

Crystal structure of the periplasmic region of MacB from E. coli

• PDB DOI: https://doi.org/10.2210/pdb5C59/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli 536
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-06-19 Released: 2016-06-22 
• Deposition Author(s): Ha, N.C., Kim, J.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.306 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.247 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.251 (Depositor) 

Literature

Crystal structure of the periplasmic region of MacB from E. coli

Ha, N.C., Kim, J.S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Biological Assembly 5  

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

Biological assembly 5 assigned by authors.

Biological Assembly 6  

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

Biological assembly 6 assigned by authors.

Biological Assembly 7  

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

Biological assembly 7 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 179.19 kDa 
• Atom Count: 8,632 
• Modeled Residue Count: 1,096 
• Deposited Residue Count: 1,582 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrolide export ATP-binding/permease protein MacB	A, B, C, D, E, F, G	226	Escherichia coli 536	Mutation(s): 0  Gene Names: macB, ECP_0894 EC: 3.6.3 (PDB Primary Data), 7.6.2 (UniProt)
UniProt
Find proteins for Q0TJH0 (Escherichia coli O6:K15:H31 (strain 536 / UPEC)) Explore Q0TJH0  Go to UniProtKB:  Q0TJH0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.306 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.247 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.251 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.144	α = 90
b = 78.565	β = 99.72
c = 137.922	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-06-22 
Deposition Author(s): Ha, N.C., Kim, J.S.

Revision History  

• Version 1.0: 2016-06-22
  Type: Initial release
  
• Version 1.1: 2020-02-19
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Structure summary