7BNG | pdb_00007bng

Complex structure of SH3b domain with L-canavanine

PDB DOI: https://doi.org/10.2210/pdb7BNG/pdb

Classification: CELL ADHESION
Organism(s): Staphylococcus simulans
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-01-22 Released: 2021-02-17
Deposition Author(s): Malecki, P.H., Sabala, I.
Funding Organization(s): Foundation for Polish Science

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free:
0.200 (Depositor), 0.210 (DCC)
R-Value Work:
0.159 (Depositor), 0.170 (DCC)
R-Value Observed:
0.161 (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

Complex structure of SH3b domain with L-canavanine

Malecki, P.H., Sabala, I.

To be published.

Macromolecule Content

Total Structure Weight: 22.48 kDa
Atom Count: 1,858
Modeled Residue Count: 192
Deposited Residue Count: 192
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysostaphin	A, B	96	Staphylococcus simulans	Mutation(s): 0 Gene Names: HMPREF3215_01322 EC: 3.4.24.75

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GGB (Subject of Investigation/LOI) Query on GGB Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	L-CANAVANINE C₅ H₁₂ N₄ O₃ FSBIGDSBMBYOPN-VKHMYHEASA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain H [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain H [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain H [auth A]	F [auth A], G [auth A], H [auth A], I [auth A], J [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain E [auth A] mmCIF format, chain C [auth A] mmCIF format, chain E [auth A]	C [auth A], E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free: 0.200 (Depositor), 0.210 (DCC)
R-Value Work: 0.159 (Depositor), 0.170 (DCC)
R-Value Observed: 0.161 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.898	α = 90
b = 55.232	β = 93.41
c = 48.994	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASES	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-02-17

Deposition Author(s):

Malecki, P.H.

Sabala, I.

Funding Organization	Location	Grant Number
Foundation for Polish Science	Poland	POIR.04.04.00-00-3D8D/16-00

Revision History (Full details and data files)

Version 1.0: 2021-02-17
Type: Initial release
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Database references
Version 2.1: 2024-01-31
Changes: Refinement description