5L4X | pdb_00005l4x

Crystal structure of FimH lectin domain in complex with 4-Deoxy-Heptylmannoside

• PDB DOI: https://doi.org/10.2210/pdb5L4X/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-05-26 Released: 2017-06-21 
• Deposition Author(s): Jakob, R.P., Zihlmann, P., Rabbani, S., Maier, T., Ernst, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.204 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

High-Affinity Carbohydrate-Lectin Interactions: How Nature Makes it Possible

Zihlmann, P., Jiang, X., Sager, C.P., Fiege, B., Jakob, R.P., Siegrist, S., Zalewski, A., Rabbani, S., Eris, D., Silbermann, M., Pang, L., Muhlethaler, T., Sharpe, T., Maier, T., Ernst, B.

To be published.

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)

Macromolecule Content

• Total Structure Weight: 34.36 kDa 
• Atom Count: 2,819 
• Modelled Residue Count: 316 
• Deposited Residue Count: 316 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein FimH	A, B	158	Escherichia coli K-12	Mutation(s): 0  Gene Names: fimH, b4320, JW4283
UniProt
Find proteins for P08191 (Escherichia coli (strain K12)) Explore P08191  Go to UniProtKB:  P08191

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6KU	C [auth A], D [auth B]	heptyl 4-deoxy-4-deoxy-alpha-D-mannopyranoside C13 H26 O5 JEMWDTFNPZXRJX-CYDGBPFRSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.204 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.079	α = 90
b = 68.38	β = 90
c = 95.629	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-06-21 
Deposition Author(s): Jakob, R.P., Zihlmann, P., Rabbani, S., Maier, T., Ernst, B.

Revision History  

• Version 1.0: 2017-06-21
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Derived calculations, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-13
  Changes: Structure summary