5ZJV | pdb_00005zjv

Crystal structure of the catalytic domain of MCR-1 (cMCR-1) in complex with xylose

• PDB DOI: https://doi.org/10.2210/pdb5ZJV/pdb

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


• Deposited: 2018-03-22 Released: 2018-04-25 
• Deposition Author(s): Liu, Z.X., Han, Z., Yu, X.L., Wen, G., Zeng, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 
  0.186 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the Catalytic Domain of MCR-1 (cMCR-1) in Complex with d-Xylose

Liu, Z.X., Han, Z., Yu, X.L., Wen, G., Zeng, C.

(2018) Crystals (Basel) 8

• DOI: https://doi.org/10.3390/cryst8040172

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 37.33 kDa 
• Atom Count: 3,188 
• Modeled Residue Count: 331 
• Deposited Residue Count: 331 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable phosphatidylethanolamine transferase Mcr-1	A	331	Escherichia coli	Mutation(s): 0  Gene Names: mcr1, mcr-1, APZ14_31440 EC: 2.7 (PDB Primary Data), 2.7.8.43 (UniProt)
UniProt
Find proteins for A0A0R6L508 (Escherichia coli) Explore A0A0R6L508  Go to UniProtKB:  A0A0R6L508

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LXC	B [auth A]	beta-L-xylopyranose C5 H10 O5 SRBFZHDQGSBBOR-QTBDOELSSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	A	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free:  0.186 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.58	α = 90
b = 73.13	β = 90
c = 82.3	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-04-25 
Deposition Author(s): Liu, Z.X., Han, Z., Yu, X.L., Wen, G., Zeng, C.

Revision History  

• Version 1.0: 2018-04-25
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2023-11-22
  Changes: Advisory, Data collection, Database references, Refinement description, Structure summary
• Version 1.3: 2024-11-20
  Changes: Structure summary