5ZJV

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free: 0.186
R-Value Work: 0.148
R-Value Observed: 0.150

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
UniProt
Find proteins for A0A0R6L508 (Escherichia coli) Explore A0A0R6L508 Go to UniProtKB: A0A0R6L508
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0R6L508
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LXC Query on LXC Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	beta-L-xylopyranose C₅ H₁₀ O₅ SRBFZHDQGSBBOR-QTBDOELSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO Query on 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
R-Value Work: 0.148
R-Value Observed: 0.150
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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-04-25

Deposition Author(s):

Revision History (Full details and data files)

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

Prepare Data

Validate Data

Deposit Data

Help and Resources

5ZJV

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

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)