BMRB Entry 5483

Name: NMR structure of AmpD, an N-acetylmuramyl-L-alanine amidase.
Published: 2003-04-23

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

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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: NMR structure of AmpD, an N-acetylmuramyl-L-alanine amidase. PubMed: 12654266

Deposition date: 2002-07-30 Original release date: 2003-04-23

Authors: Liepinsh, Edvards; Genereux, Catherine; Dehareng, Dominique; Joris, Bernard; Otting, Gottfried

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).

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

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

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

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

Data sets:

assigned_chemical_shifts
- shift_set_1

Data type	Count
1H chemical shifts	1256
13C chemical shifts	630
15N chemical shifts	202

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	AmpD 1	1
2	Zinc ion	2

Entities:

Entity 1, AmpD 1 187 residues - 19805 Da.

1

MET

LEU

ASP

GLU

GLY

TRP

LEU

ALA

GLU

2

ALA

ARG

VAL

PRO

SER

PRO

HIS

TYR

ASP

3

CYS

ARG

PRO

ASP

GLU

ASN

PRO

SER

LEU

4

LEU

VAL

HIS

ASN

ILE

SER

LEU

PRO

5

GLY

GLU

PHE

GLY

PRO

TRP

ILE

ASP

ALA

6

LEU

PHE

THR

GLY

THR

ILE

ASP

PRO

ASN

ALA

7

HIS

PRO

TYR

PHE

ALA

GLY

ILE

ALA

HIS

LEU

8

ARG

VAL

SER

ALA

HIS

CYS

LEU

ILE

ARG

9

ASP

GLY

GLU

ILE

VAL

GLN

TYR

VAL

PRO

PHE

10

ASP

LYS

ARG

ALA

TRP

HIS

ALA

GLY

VAL

SER

11

SER

TYR

GLN

GLY

ARG

GLU

ARG

CYS

ASN

ASP

12

PHE

SER

ILE

GLY

ILE

GLU

LEU

GLU

GLY

THR

13

ASP

THR

LEU

ALA

TYR

THR

ASP

ALA

GLN

TYR

14

GLN

LEU

ALA

VAL

THR

ASN

ALA

LEU

15

ILE

THR

ARG

TYR

PRO

ALA

ILE

ALA

ASN

16

MET

THR

GLY

HIS

CYS

ASN

ILE

ALA

PRO

GLU

17

ARG

LYS

THR

ASP

PRO

GLY

PRO

SER

PHE

ASP

18

TRP

ALA

ARG

PHE

ARG

ALA

LEU

VAL

THR

PRO

19

SER

HIS

LYS

GLU

MET

THR

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:

Name	Sample	Sample state	Sample conditions
2D 1H-1H DQF-COSY	not available	not available	Ex-cond_1
2D 1H-1H HOHAHA	not available	not available	Ex-cond_1
2D 1H-1H NOESY	not available	not available	Ex-cond_1
3D HNHB	not available	not available	Ex-cond_1
2D 1H-15N HSQC	not available	not available	Ex-cond_1
2D 1H-13C HSQC	not available	not available	Ex-cond_1
3D 1H-1H-15N TOCSY	not available	not available	Ex-cond_1
3D 1H-1H-15N NOESY	not available	not available	Ex-cond_1
3D HNCO	not available	not available	Ex-cond_1
3D HNCA	not available	not available	Ex-cond_1
3D HN(CO)CA	not available	not available	Ex-cond_1
3D CBCA(CO)NH	not available	not available	Ex-cond_1
3D HNCO(CO)NH	not available	not available	Ex-cond_1
3D H(C)CH-TOCSY	not available	not available	Ex-cond_1
3D HC(C)H-TOCSY	not available	not available	Ex-cond_1

Software:

XWINNMR - spectral processing

PROSA - spectral processing

NMR spectrometers:

Bruker DMX 600 MHz
Varian UnityPlus 800 MHz

PDB	1J3G 2Y28 2Y2B 2Y2C 2Y2D 2Y2E
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

Biological Magnetic Resonance Data Bank