6YF6 | pdb_00006yf6

EclA C-terminal domain; sugar-binding protein

PDB DOI: https://doi.org/10.2210/pdb6YF6/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Enterobacter cloacae subsp. cloacae ATCC 13047
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-03-26 Released: 2021-04-07
Deposition Author(s): Koehnke, J., Sikandar, A.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.237 (Depositor), 0.242 (DCC)
R-Value Work:
0.190 (Depositor), 0.199 (DCC)
R-Value Observed:
0.192 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

EclA C-terminal domain; sugar-binding protein

Koehnke, J., Sikandar, A.

To be published.

Macromolecule Content

Total Structure Weight: 32.52 kDa
Atom Count: 2,471
Modeled Residue Count: 280
Deposited Residue Count: 288
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galactose-binding lectin	A, B	144	Enterobacter cloacae subsp. cloacae ATCC 13047	Mutation(s): 0 Gene Names: ECL_04191
UniProt
Find proteins for A0A0H3CQ33 (Enterobacter cloacae subsp. cloacae (strain ATCC 13047 / DSM 30054 / NBRC 13535 / NCTC 10005 / WDCM 00083 / NCDC 279-56)) Explore A0A0H3CQ33 Go to UniProtKB: A0A0H3CQ33
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H3CQ33
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SFU Query on SFU Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	methyl 1-seleno-alpha-L-fucopyranoside C₇ H₁₄ O₄ Se VHTNTJQSKJZERS-XUVCUMPTSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], G [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.237 (Depositor), 0.242 (DCC)
R-Value Work: 0.190 (Depositor), 0.199 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.512	α = 90
b = 63.671	β = 90
c = 134.009	γ = 90

Software Package:

Software Name	Purpose
Aimless	refinement
PHENIX	refinement
xia2	data reduction
Aimless	data scaling
AutoSol	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-04-07

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	KO4116_3_1

Revision History (Full details and data files)

Version 1.0: 2021-04-07
Type: Initial release
Version 1.1: 2024-05-15
Changes: Data collection, Database references

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