BMRB Entry 34446

Name: Bam_5924 docking domain
Published: 2020-08-06

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PDB ID: 6tdd
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34446
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Bam_5924 docking domain

Deposition date:

2019-11-08

Original release date:

2020-08-06

Authors:

Risser, F.; Chagot, B.

Citation:

Citation: Risser, F.; Collin, S.; Dos Santos-Morais, R.; Gruez, A.; Chagot, B.; Weissman, K.. "Towards improved understanding of intersubunit interactions in modular polyketide biosynthesis: Docking in the enacyloxin IIa polyketide synthase" J. Struct. Biol. 212, 107581-107581 (2020).
PubMed: 32717326

Assembly members:

Assembly members:
entity_1, polymer, 45 residues, 5026.728 Da.

Natural source:

Natural source: Common Name: Burkholderia ambifaria AMMD Taxonomy ID: 339670 Superkingdom: Bacteria Kingdom: not available Genus/species: Burkholderia ambifaria

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pBG102

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GPGSMNKPTSSDGWKDDYLS RLSRLSKNQLMALALKLKQQ QLEQG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	386
15N chemical shifts	100
1H chemical shifts	650

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1, 1	1
2	entity_1, 2	1

Entities:

Entity 1, entity_1, 1 45 residues - 5026.728 Da.

1

GLY

PRO

GLY

SER

MET

ASN

LYS

PRO

THR

SER

2

SER

ASP

GLY

TRP

LYS

ASP

TYR

LEU

SER

3

ARG

LEU

SER

ARG

LEU

SER

LYS

ASN

GLN

LEU

4

MET

ALA

LEU

ALA

LEU

LYS

LEU

LYS

GLN

5

GLN

LEU

GLU

GLN

GLY

Samples:

sample_1: entity_1 mM; sodium phosphate 100 mM

sample_conditions_1: ionic strength: 0.1 M; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1

Software:

TopSpin, Bruker Biospin - collection

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

Sparky, Goddard - chemical shift assignment, peak picking

Amber, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

NMR spectrometers:

Bruker DRX 600 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks