BMRB Entry 5483

Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR5483

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Title:
NMR structure of AmpD, an N-acetylmuramyl-L-alanine amidase.
Deposition date:
2002-07-30
Original release date:
2003-04-23
Authors:
Liepinsh, Edvards; Genereux, Catherine; Dehareng, Dominique; Joris, Bernard; Otting, Gottfried
Citation:

Citation: Liepinsh, Edvards; Genereux, Catherine; Dehareng, Dominique; Joris, Bernard; Otting, Gottfried. "NMR Structure of Citrobacter freundii AmpD, Comparison with Bacteriophage T7 Lysozyme and Homology with PGRP Domains"  J. Mol. Biol. 327, 833-842 (2003).
PubMed: 12654266

Assembly members:

Assembly members:
single chain biopolymer, polymer, 187 residues, 19805 Da.
ZN, non-polymer, 65.409 Da.

Natural source:

Natural source:   Common Name: not available   Taxonomy ID: 546   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Citrobacter freundii

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET-3a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
single chain biopolymer: MLLDEGWLAEARRVPSPHYD CRPDDENPSLLVVHNISLPP GEFGGPWIDALFTGTIDPNA HPYFAGIAHLRVSAHCLIRR DGEIVQYVPFDKRAWHAGVS SYQGRERCNDFSIGIELEGT DTLAYTDAQYQQLAAVTNAL ITRYPAIANNMTGHCNIAPE RKTDPGPSFDWARFRALVTP SSHKEMT

Data sets:
Data typeCount
1H chemical shifts1256
13C chemical shifts630
15N chemical shifts202

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1AmpD 11
2Zinc ion2

Entities:

Entity 1, AmpD 1 187 residues - 19805 Da.

1   METLEULEUASPGLUGLYTRPLEUALAGLU
2   ALAARGARGVALPROSERPROHISTYRASP
3   CYSARGPROASPASPGLUASNPROSERLEU
4   LEUVALVALHISASNILESERLEUPROPRO
5   GLYGLUPHEGLYGLYPROTRPILEASPALA
6   LEUPHETHRGLYTHRILEASPPROASNALA
7   HISPROTYRPHEALAGLYILEALAHISLEU
8   ARGVALSERALAHISCYSLEUILEARGARG
9   ASPGLYGLUILEVALGLNTYRVALPROPHE
10   ASPLYSARGALATRPHISALAGLYVALSER
11   SERTYRGLNGLYARGGLUARGCYSASNASP
12   PHESERILEGLYILEGLULEUGLUGLYTHR
13   ASPTHRLEUALATYRTHRASPALAGLNTYR
14   GLNGLNLEUALAALAVALTHRASNALALEU
15   ILETHRARGTYRPROALAILEALAASNASN
16   METTHRGLYHISCYSASNILEALAPROGLU
17   ARGLYSTHRASPPROGLYPROSERPHEASP
18   TRPALAARGPHEARGALALEUVALTHRPRO
19   SERSERHISLYSGLUMETTHR

Entity 2, Zinc ion - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: single chain biopolymer 0.3 mM; ZINC (II) ION mM

sample_2: single chain biopolymer, [U-95% 15N], 0.3 mg/ml; ZINC (II) ION mM

sample_3: single chain biopolymer, [U-95% 13C; U-95% 15N], 0.3 mM; ZINC (II) ION mM

Ex-cond_1: pH: 5.5 na; temperature: 304 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H DQF-COSYnot availablenot availableEx-cond_1
2D 1H-1H HOHAHAnot availablenot availableEx-cond_1
2D 1H-1H NOESYnot availablenot availableEx-cond_1
3D HNHBnot availablenot availableEx-cond_1
2D 1H-15N HSQCnot availablenot availableEx-cond_1
2D 1H-13C HSQCnot availablenot availableEx-cond_1
3D 1H-1H-15N TOCSYnot availablenot availableEx-cond_1
3D 1H-1H-15N NOESYnot availablenot availableEx-cond_1
3D HNCOnot availablenot availableEx-cond_1
3D HNCAnot availablenot availableEx-cond_1
3D HN(CO)CAnot availablenot availableEx-cond_1
3D CBCA(CO)NHnot availablenot availableEx-cond_1
3D HNCO(CO)NHnot availablenot availableEx-cond_1
3D H(C)CH-TOCSYnot availablenot availableEx-cond_1
3D HC(C)H-TOCSYnot availablenot availableEx-cond_1

Software:

XWINNMR - spectral processing

PROSA - spectral processing

NMR spectrometers:

  • Bruker DMX 600 MHz
  • Varian UnityPlus 800 MHz

Related Database Links:

PDB
DBJ GAL38703
EMBL CAA78390 CDL37434
GB EEH95053 EFE07580 EHL83818 EJF22884 EKS57727
REF WP_003018719 WP_003829500 WP_006686718 WP_008786207 WP_016151712
SP P82974
AlphaFold P82974

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