4HJV

Crystal structure of E. coli MltE with bound bulgecin and murodipeptide

• PDB DOI: https://doi.org/10.2210/pdb4HJV/pdb
• Entry: 4HJV supersedes: 3T4I

• Classification: LYASE/LYASE INHIBITOR
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-10-14 Released: 2012-10-24 
• Deposition Author(s): Fibriansah, G., Gliubich, F.I., Thunnissen, A.-M.W.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.203 
• R-Value Work: 0.163 
• R-Value Observed: 0.167 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

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

Biological assembly 5 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 115.03 kDa 
• Atom Count: 7,814 
• Modelled Residue Count: 921 
• Deposited Residue Count: 1,015 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endo-type membrane-bound lytic murein transglycosylase A	A, B, C, D, E	203	Escherichia coli K-12	Mutation(s): 0  Gene Names: emtA, mltE, sltZ, ycgP, b1193, JW5821 EC: 4.2.2
UniProt
Find proteins for P0C960 (Escherichia coli (strain K12)) Explore P0C960  Go to UniProtKB:  P0C960

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-beta-muramic acid	F, G, H	2		N/A
Glycosylation Resources
GlyTouCan:  G99515FY GlyCosmos:  G99515FY

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BLG	I [auth A], J [auth B], L [auth C], N [auth D]	4-O-(4-O-SULFONYL-N-ACETYLGLUCOSAMININYL)-5-METHYLHYDROXY-L-PROLINE-TAURINE C16 H30 N3 O14 S2 RPNZWZDLNYCCIG-HMMVDTEZSA-O
SO4	K [auth B], M [auth C], O [auth E]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.203 
• R-Value Work: 0.163 
• R-Value Observed: 0.167 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.778	α = 90
b = 94.853	β = 90
c = 162.016	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-24 
Deposition Author(s): Fibriansah, G., Gliubich, F.I., Thunnissen, A.-M.W.H.
• This entry supersedes: 3T4I

Revision History  

• Version 1.0: 2012-10-24
  Type: Initial release
  
• Version 1.1: 2012-10-31
  Changes: Database references
• Version 1.2: 2012-12-26
  Changes: Database references
• Version 1.3: 2017-11-15
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-09-20
  Changes: Data collection, Database references, Refinement description, Structure summary