BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules 		Member of WWPDB

BMRB Entry 19876

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19876
MolProbity Validation Chart

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Title: 3D structure of YmoB. A modulator of biofilm formation.

Deposition date: 2014-03-26 Original release date: 2015-03-30

Authors: Marimon, Oriol; Cordeiro, Tiago; Amata, Irene; Pons, Miquel

Citation: Marimon, Oriol; Cordeiro, Tiago; Amata, Irene; Mayzel, Maxim; Orekhov, Vladislav; Wood, Thomas; Pons, Miquel. "TomB/YmoB proteins: structure and function in biofilm regulation."  Not known ., .-..

Assembly members:
entity, polymer, 133 residues, 14191.914 Da.

Natural source:   Common Name: enterobacteria   Taxonomy ID: 630   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Yersinia enterocolitica

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

Entity Sequences (FASTA):
entity: MSHHHHHHSMGMDEYSPKRH DVAQLKFLCESLYDEGIATL GDSHHGWVNDPTSAVNLQLN DLIEHIASFVMSFKIKYPDD GDLSELVEEYLDDTYTLFSS YGINDPELQRWQKTKERLFR LFSGEYISTLMKT

Data sets:
Data typeCount
13C chemical shifts505
15N chemical shifts123
1H chemical shifts866

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1YmoB-C117S1

Entities:

Entity 1, YmoB-C117S 133 residues - 14191.914 Da.

1   METSERHISHISHISHISHISHISSERMET
2   GLYMETASPGLUTYRSERPROLYSARGHIS
3   ASPVALALAGLNLEULYSPHELEUCYSGLU
4   SERLEUTYRASPGLUGLYILEALATHRLEU
5   GLYASPSERHISHISGLYTRPVALASNASP
6   PROTHRSERALAVALASNLEUGLNLEUASN
7   ASPLEUILEGLUHISILEALASERPHEVAL
8   METSERPHELYSILELYSTYRPROASPASP
9   GLYASPLEUSERGLULEUVALGLUGLUTYR
10   LEUASPASPTHRTYRTHRLEUPHESERSER
11   TYRGLYILEASNASPPROGLULEUGLNARG
12   TRPGLNLYSTHRLYSGLUARGLEUPHEARG
13   LEUPHESERGLYGLUTYRILESERTHRLEU
14   METLYSTHR

Samples:

sample_1: YmoB-C117S 1 mM; sodium phosphate 20 mM; sodium chloride 150 mM; TCEP 1 mM; EDTA 0.2 mM; sodium azide 0.1%; H2O 90%; D2O 10%

sample_2: YmoB-C117S, [U-100% 15N], 1 mM; sodium phosphate 20 mM; sodium chloride 150 mM; TCEP 1 mM; EDTA 0.2 mM; sodium azide 0.1%; H2O 90%; D2O 10%

sample_3: YmoB-C117S, [U-100% 13C; U-100% 15N], 1 mM; sodium phosphate 20 mM; sodium chloride 150 mM; TCEP 1 mM; EDTA 0.2 mM; sodium azide 0.1%; H2O 90%; D2O 10%

sample_4: YmoB-C117S, [U-100% 13C; U-100% 15N], 1 mM; sodium phosphate 20 mM; sodium chloride 150 mM; TCEP 1 mM; EDTA 0.2 mM; sodium azide 0.1%; H2O 90%; D2O 10%

sample_5: YmoB-C117S, [U-10% 13C; U-100% 15N], 1 mM; sodium phosphate 20 mM; sodium chloride 150 mM; TCEP 1 mM; EDTA 0.2 mM; sodium azide 0.1%; H2O 90%; D2O 10%

sample_conditions_1: pH: 7.00; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
3D HNCOsample_3isotropicsample_conditions_1
3D HN(CO)CAsample_3isotropicsample_conditions_1
3D CBCA(CO)NHsample_3isotropicsample_conditions_1
2D 1H-13C HSQCsample_3isotropicsample_conditions_1
2D 1H-13C HSQC aliphatic Constant Timesample_5isotropicsample_conditions_1
3D HBHA(CO)NHsample_3isotropicsample_conditions_1
3D HNCACBsample_3isotropicsample_conditions_1
2D 1H-15N HSQCsample_4isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_3isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_4isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_4isotropicsample_conditions_1
3D HCCH-TOCSYsample_4isotropicsample_conditions_1
3D HccH-TOCSYsample_4isotropicsample_conditions_1
3D 1H-15N NOESYsample_3isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_4isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_4isotropicsample_conditions_1

Software:

TOPSPIN v2.0 and 3.0, Bruker Biospin - collection

VNMRJ v3.2, Varian - collection

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

MddNMR, V. Orekhov, V. Jaravine, M. Mayzel, K. Kazimierczuk, Swedish NMR Center, University of Gothenburg - processing

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - data analysis

NMRView, Johnson, One Moon Scientific - data analysis

CARA v1.9.0 Beta 3, (c) 2000-2010 by Rochus Keller and others - chemical shift assignment, peak picking

Unio'10 vVersion 2.0.2, 2002-2011 Torsten Herrmann - chemical shift assignment

TALOS v+, Cornilescu, Delaglio and Bax - data analysis

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

CNS v1.2.1, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

ProcheckNMR, Laskowski and MacArthur - data analysis

Molmol, Koradi, Billeter and Wuthrich - data analysis

PyMol, Schr dinger, LLC. - data analysis

NMR spectrometers:

  • Bruker DRX 800 MHz
  • Varian INOVA 900 MHz
  • Varian INOVA 800 MHz

Related Database Links:

PDB
EMBL CAL13149 CBX70720 CBY26149 CCO69635 CCQ41626
GB AAQ90016 ADZ41643 AHM72673 AJI85062 AJJ21754
REF WP_005163463 WP_005167670 WP_050077354 YP_001007296

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