3FWS | pdb_00003fws

Crystal Structure of the CBS domains from the Bacillus subtilis CcpN repressor complexed with AppNp, phosphate and magnesium ions

PDB DOI: https://doi.org/10.2210/pdb3FWS/pdb

Classification: TRANSCRIPTION
Organism(s): Bacillus subtilis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-01-19 Released: 2010-01-26
Deposition Author(s): Chaix, D., Arold, S., Hoh, F., Declerck, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free:
0.262 (Depositor), 0.270 (DCC)
R-Value Work:
0.189 (Depositor), 0.203 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Ligand recognition by the energy sensor domain of the CcpN repressor

Chaix, D., de Guillen, K., Coq, D.L., Hoh, F., Roumestand, C., Aymerich, S., Arold, S.T., Declerck, N.

To be published.

Macromolecule Content

Total Structure Weight: 37.31 kDa
Atom Count: 2,446
Modeled Residue Count: 291
Deposited Residue Count: 318
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YqzB protein	A, B	159	Bacillus subtilis	Mutation(s): 0 Gene Names: yqzB
UniProt
Find proteins for O34994 (Bacillus subtilis (strain 168)) Explore O34994 Go to UniProtKB: O34994
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O34994
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain C [auth A]	C [auth A], G [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain D [auth A]	D [auth A], H [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free: 0.262 (Depositor), 0.270 (DCC)
R-Value Work: 0.189 (Depositor), 0.203 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.025	α = 90
b = 103.969	β = 90
c = 98.387	γ = 90

Software Package:

Software Name	Purpose
SOLVE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-01-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-01-26
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description

3FWS | pdb_00003fws

Crystal Structure of the CBS domains from the Bacillus subtilis CcpN repressor complexed with AppNp, phosphate and magnesium ions

Literature

Ligand recognition by the energy sensor domain of the CcpN repressor

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand