2WB4

activated diguanylate cyclase PleD in complex with c-di-GMP

PDB DOI: https://doi.org/10.2210/pdb2WB4/pdb

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

Deposited: 2009-02-20 Released: 2010-04-21
Deposition Author(s): Wassmann, P., Schirmer, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.268
R-Value Work: 0.239
R-Value Observed: 0.241

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of Activated Pled, Identification of Dimerization and Catalysis Relevant Regulatory Mechanisms

Wassmann, P., Massa, C., Zaehringer, F., Schirmer, T.

To be published.

Macromolecule Content

Total Structure Weight: 104.71 kDa
Atom Count: 7,214
Modelled Residue Count: 899
Deposited Residue Count: 918
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DIGUANYLATE CYCLASE	A, B	459	Caulobacter vibrioides CB15	Mutation(s): 0 EC: 2.7.7.65 (PDB Primary Data), 4.6.1 (PDB Primary Data)
UniProt
Find proteins for B8GZM2 (Caulobacter vibrioides (strain NA1000 / CB15N)) Explore B8GZM2 Go to UniProtKB: B8GZM2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B8GZM2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
C2E Query on C2E Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B]	E [auth A], F [auth A], K [auth B], L [auth B], M [auth B]	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 E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain O [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain O [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain O [auth B]	G [auth A], H [auth A], O [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain O [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain O [auth B]
BEF Query on BEF Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain I [auth B]	C [auth A], I [auth B]	BERYLLIUM TRIFLUORIDE ION Be F₃ OGIAHMCCNXDTIE-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain J [auth B] SDF format, chain N [auth B] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth B] mmCIF format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain N [auth B]	D [auth A], J [auth B], N [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Focus chain N [auth B] Interactions & Density Focus chain D [auth A] Focus chain J [auth B] Focus chain N [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.268
R-Value Work: 0.239
R-Value Observed: 0.241
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.56	α = 90
b = 127.43	β = 90
c = 88.13	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-04-21

Deposition Author(s):

Wassmann, P.

Schirmer, T.

Revision History (Full details and data files)

Version 1.0: 2010-04-21
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary