7B0E | pdb_00007b0e

Crystal structure of SmbA loop deletion mutant

PDB DOI: https://doi.org/10.2210/pdb7B0E/pdb

Classification: SIGNALING PROTEIN
Organism(s): Caulobacter vibrioides CB15
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-11-19 Released: 2021-12-01
Deposition Author(s): Dubey, B.N., Schirmer, T.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.177 (Depositor), 0.180 (DCC)
R-Value Work:
0.148 (Depositor), 0.150 (DCC)
R-Value Observed:
0.149 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

High-resolution crystal structure of loop deletion mutant SmbA bound to a monomeric c-di-GMP

Dubey, B.N., Shyp, V., Jenal, U., Schirmer, T.

To be published.

Macromolecule Content

Total Structure Weight: 33.64 kDa
Atom Count: 2,479
Modeled Residue Count: 270
Deposited Residue Count: 291
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SmbA	A	291	Caulobacter vibrioides CB15	Mutation(s): 0 Gene Names: CC_2504
UniProt
Find proteins for Q9A5E6 (Caulobacter vibrioides (strain ATCC 19089 / CIP 103742 / CB 15)) Explore Q9A5E6 Go to UniProtKB: Q9A5E6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9A5E6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
C2E (Subject of Investigation/LOI) Query on C2E Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) C₂₀ H₂₄ N₁₀ O₁₄ P₂ PKFDLKSEZWEFGL-MHARETSRSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain S [auth A] SDF format, chain R [auth A] SDF format, chain Q [auth A] MOL2 format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain S [auth A] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A]	Q [auth A], R [auth A], S [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Interactions & Density Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A]	O [auth A], P [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain O [auth A] Focus chain P [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.177 (Depositor), 0.180 (DCC)
R-Value Work: 0.148 (Depositor), 0.150 (DCC)
R-Value Observed: 0.149 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.04	α = 90
b = 56.04	β = 90
c = 205.068	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-12-01

Deposition Author(s):

Dubey, B.N.

Schirmer, T.

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	31003A_166652

Revision History (Full details and data files)

Version 1.0: 2021-12-01
Type: Initial release
Version 2.0: 2022-09-07
Type: Coordinate replacement
Reason: Occupancy of atoms on special symmetry positions
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Refinement description, Source and taxonomy, Structure summary
Version 2.1: 2024-01-31
Changes: Data collection, Refinement description