5L4T | pdb_00005l4t

Crystal structure of FimH lectin domain in complex with 2-Deoxy-Heptylmannoside

PDB DOI: https://doi.org/10.2210/pdb5L4T/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.218 (Depositor), 0.222 (DCC)
R-Value Work:
0.201 (Depositor), 0.203 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 2.3 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 34.36 kDa
Atom Count: 2,868
Modeled Residue Count: 316
Deposited Residue Count: 316
Unique protein chains: 1

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P08191
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6LS Query on 6LS Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	heptyl 2-deoxy-alpha-D-mannopyranoside C₁₃ H₂₆ O₅ IRECALVMQPMJAW-NDBYEHHHSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.218 (Depositor), 0.222 (DCC)
R-Value Work: 0.201 (Depositor), 0.203 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.76	α = 90
b = 68.57	β = 90
c = 96.11	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2017-06-21

Deposition Author(s):

Revision History (Full details and data files)

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: 2020-08-05
Changes: Derived calculations, Structure summary
Version 2.2: 2024-01-10
Changes: Data collection, Database references, Refinement description
Version 2.3: 2024-11-06
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.