6K6T | pdb_00006k6t

Crystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - c-di-IMP bound form

PDB DOI: https://doi.org/10.2210/pdb6K6T/pdb

Classification: HYDROLASE
Organism(s): Vibrio cholerae O395
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2019-06-04 Released: 2020-06-17
Deposition Author(s): Yadav, M., Pal, K., Sen, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.252 (Depositor), 0.256 (DCC)
R-Value Work:
0.197 (Depositor), 0.201 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - c-di-IMP bound form

Yadav, M., Pal, K., Sen, U.

To be published.

Macromolecule Content

Total Structure Weight: 119.06 kDa
Atom Count: 8,196
Modeled Residue Count: 948
Deposited Residue Count: 1,028
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EAL domain protein	A, B, C, D	257	Vibrio cholerae O395	Mutation(s): 1 Gene Names: VC0395_A1247 EC: 3.1.4.1
UniProt
Find proteins for A0A0H3AJ04 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)) Explore A0A0H3AJ04 Go to UniProtKB: A0A0H3AJ04
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H3AJ04
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
C2I (Subject of Investigation/LOI) Query on C2I Download:Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain K [auth C] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain N [auth D] MOL2 format, chain K [auth C] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain N [auth D] mmCIF format, chain K [auth C] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B], K [auth C], N [auth D]	9-[(1R,6R,8R,9S,10R,15S,17R,18S)-3,9,12,18-tetrakis(oxidanyl)-3,12-bis(oxidanylidene)-17-(6-oxidanylidene-3H-purin-9-yl)-2,4,7,11,13,16-hexaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.3.0.0^{6,10}]octadecan-8-yl]-3H-purin-6-one C₂₀ H₂₂ N₈ O₁₄ P₂ VFTRASQVWRBMKD-PHSICLOESA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain O [auth D] SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain P [auth D] MOL2 format, chain O [auth D] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain P [auth D] mmCIF format, chain O [auth D] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] I [auth B] J [auth B] L [auth C] F [auth A], G [auth A], I [auth B], J [auth B], L [auth C], M [auth C], O [auth D], P [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.252 (Depositor), 0.256 (DCC)
R-Value Work: 0.197 (Depositor), 0.201 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.45	α = 90
b = 42.54	β = 94.65
c = 155.04	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-06-17

Deposition Author(s):

Yadav, M.

Pal, K.

Sen, U.

Revision History (Full details and data files)

Version 1.0: 2020-06-17
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description

6K6T | pdb_00006k6t

Crystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - c-di-IMP bound form

Literature

Crystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - c-di-IMP bound form

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Entry History

Deposition Data

Revision History (Full details and data files)