2X8O | pdb_00002x8o

Crystal Structure of CbpF in complex with Atropine by soaking

PDB DOI: https://doi.org/10.2210/pdb2X8O/pdb

Classification: CHOLINE-BINDING PROTEIN
Organism(s): Streptococcus pneumoniae R6
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-03-10 Released: 2011-04-06
Deposition Author(s): Silva-Martin, N., Hermoso, J.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free:
0.260 (Depositor), 0.261 (DCC)
R-Value Work:
0.222 (Depositor), 0.222 (DCC)
R-Value Observed:
0.222 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of Cbpf in Complex with Atropine by Soaking

Silva-Martin, N., Hermoso, J.A., Sanz, J.M.

To be published.

Macromolecule Content

Total Structure Weight: 37.99 kDa
Atom Count: 2,905
Modeled Residue Count: 311
Deposited Residue Count: 311
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CHOLINE-BINDING PROTEIN F	A	311	Streptococcus pneumoniae R6	Mutation(s): 0
UniProt
Find proteins for Q8DR52 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6)) Explore Q8DR52 Go to UniProtKB: Q8DR52
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8DR52
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OIN Query on OIN Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain D [auth A] MOL2 format, chain G [auth A] MOL2 format, chain D [auth A] mmCIF format, chain G [auth A] mmCIF format, chain D [auth A]	D [auth A], G [auth A]	(1R,5S)-8-METHYL-8-AZABICYCLO[3.2.1]OCT-3-YL (2R)-3-HYDROXY-2-PHENYLPROPANOATE C₁₇ H₂₃ N O₃ RKUNBYITZUJHSG-QKPAOTATSA-N		Interactions Focus chain D [auth A] Focus chain G [auth A] Interactions & Density Focus chain D [auth A] Focus chain G [auth A]
CHT Query on CHT Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] MOL2 format, chain B [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] mmCIF format, chain B [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A]	B [auth A] H [auth A] I [auth A] L [auth A] M [auth A] B [auth A], H [auth A], I [auth A], L [auth A], M [auth A], N [auth A]	CHOLINE ION C₅ H₁₄ N O OEYIOHPDSNJKLS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain B [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], J [auth A], K [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth A] Focus chain K [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free: 0.260 (Depositor), 0.261 (DCC)
R-Value Work: 0.222 (Depositor), 0.222 (DCC)
R-Value Observed: 0.222 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.409	α = 90
b = 116.752	β = 90
c = 73.889	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
XDS	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-04-06

Deposition Author(s):

Silva-Martin, N.

Hermoso, J.A.

Revision History (Full details and data files)

Version 1.0: 2011-04-06
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description

2X8O | pdb_00002x8o

Crystal Structure of CbpF in complex with Atropine by soaking

Literature

Crystal Structure of Cbpf in Complex with Atropine by Soaking

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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