4XM3 | pdb_00004xm3

Tailspike protein mutant E372A of E. coli bacteriophage HK620 in complex with pentasaccharide

• PDB DOI: https://doi.org/10.2210/pdb4XM3/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Enterobacteria phage HK620
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2015-01-14 Released: 2016-01-27 
• Deposition Author(s): Gohlke, U., Broeker, N.K., Heinemann, U., Seckler, R., Barbirz, S.
• Funding Organization(s): German Research Foundation

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free: 
  0.170 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.134 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.136 (Depositor) 

Starting Model: experimental

Literature

Enthalpic cost of water removal from a hydrophobic glucose binding cavity on HK620 tailspike protein.

Gohlke, U., Broeker, N.K., Kunstmann, S., Santer, M., Heinemann, U., Lipowski, R., Seckler, R., Barbirz, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 65.94 kDa 
• Atom Count: 5,486 
• Modelled Residue Count: 599 
• Deposited Residue Count: 599 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tail spike protein	A	599	Enterobacteria phage HK620	Mutation(s): 1
UniProt
Find proteins for Q9AYY6 (Enterobacteria phage HK620) Explore Q9AYY6  Go to UniProtKB:  Q9AYY6

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-rhamnopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)]alpha-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-glucopyranose	B	6		N/A
Glycosylation Resources
GlyTouCan:  G81480NI GlyCosmos:  G81480NI

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	C [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
FMT	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
NA	K [auth A], L [auth A], M [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free:  0.170 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.134 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.136 (Depositor) 

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.354	α = 90
b = 74.354	β = 90
c = 175.187	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
ARP	model building
Coot	model building
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-01-27 
Deposition Author(s): Gohlke, U., Broeker, N.K., Heinemann, U., Seckler, R., Barbirz, S.

---

Funding Organization	Location	Grant Number
German Research Foundation	Germany	BA 4046/1-1

Revision History  

• Version 1.0: 2016-01-27
  Type: Initial release
  
• Version 1.1: 2017-09-06
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2018-04-25
  Changes: Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description, Structure summary