BMRB Entry 15055

Name: Structure for the N-terminus of chromosomal replication initiation protein dnaA from M. genitalium
Published: 2007-10-16

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PDB ID: 2jmp
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR15055
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Structure for the N-terminus of chromosomal replication initiation protein dnaA from M. genitalium

Deposition date:

2006-11-27

Original release date:

2007-10-16

Authors:

Lowery, Thomas; Pelton, Jeffrey; Wemmer, David

Citation:

Citation: Lowery, Thomas; Pelton, Jeffrey; Chandonia, John-Marc; Kim, Rosalind; Yokota, Hisao; Wemmer, David. "NMR Structure of the N-terminal domain of the replication initiator protein DnaA" J. Struct. Funct. Genomics 8, 11-17 (2007).
PubMed: 17680349

Assembly members:

Assembly members:
N_dnaA, polymer, 100 residues, 11870.441 Da.

Natural source:

Natural source: Common Name: Mycoplasma genitalium Taxonomy ID: 2097 Superkingdom: Bacteria Kingdom: not available Genus/species: Mycoplasma genitalium

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: LIC(pB3)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
N_dnaA: MEQFNAFKSLLKKHYEKTIG FHDKYIKDINRFVFKNNVLL ILLENEFARNSLNDNSEIIH LAESLYEGIKSVNFVNEQDF FFNLAKLEENSRDTLYQNSG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	403
15N chemical shifts	99
1H chemical shifts	602

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	N_dnaA	1

Entities:

Entity 1, N_dnaA 100 residues - 11870.441 Da.

1	MET	GLU	GLN	PHE	ASN	ALA	PHE	LYS	SER	LEU
2	LEU	LYS	LYS	HIS	TYR	GLU	LYS	THR	ILE	GLY
3	PHE	HIS	ASP	LYS	TYR	ILE	LYS	ASP	ILE	ASN
4	ARG	PHE	VAL	PHE	LYS	ASN	ASN	VAL	LEU	LEU
5	ILE	LEU	LEU	GLU	ASN	GLU	PHE	ALA	ARG	ASN
6	SER	LEU	ASN	ASP	ASN	SER	GLU	ILE	ILE	HIS
7	LEU	ALA	GLU	SER	LEU	TYR	GLU	GLY	ILE	LYS
8	SER	VAL	ASN	PHE	VAL	ASN	GLU	GLN	ASP	PHE
9	PHE	PHE	ASN	LEU	ALA	LYS	LEU	GLU	GLU	ASN
10	SER	ARG	ASP	THR	LEU	TYR	GLN	ASN	SER	GLY

Samples:

sample_1: N_dnaA, [U-100% 15N], 0.75 ± 0.2 mM; sodium phosphate 50 ± 10 mM; sodium chloride 100 ± 10 mM; EDTA 2 ± 1 mM; sodium azide 0.05 ± 0.01 %

sample_2: N_dnaA, [U-98% 13C; U-98% 15N], 0.75 ± 0.2 mM; sodium phosphate 50 ± 10 mM; sodium chloride 100 ± 10 mM; EDTA 2 ± 1 mM; sodium azide 0.05 ± 0.01 %

sample_3: N_dnaA 0.75 ± 0.2 mM; sodium phosphate 50 ± 10 mM; sodium chloride 100 ± 10 mM; EDTA 2 ± 1 mM; sodium azide 0.05 ± 0.01 %

sample_4: N_dnaA, [U-98% 13C; U-98% 15N], 0.75 ± 0.2 mM; sodium phosphate 50 ± 10 mM; sodium chloride 100 ± 10 mM; EDTA 2 ± 1 mM; sodium azide 0.05 ± 0.01 %

sample_5: N_dnaA, [10% 13C], 0.75 ± 0.2 mM; sodium phosphate 50 ± 10 mM; sodium chloride 100 ± 10 mM; EDTA 2 ± 1 mM; sodium azide 0.05 ± 0.01 %

sample_conditions_1: pH: 6.8; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_2	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_2	isotropic	sample_conditions_1
3D HNCACB	sample_2	isotropic	sample_conditions_1
3D HNCO	sample_2	isotropic	sample_conditions_1
3D C(CO)NH	sample_2	isotropic	sample_conditions_1
3d HN(CA)CO	sample_2	isotropic	sample_conditions_1
3D HNHA	sample_1	isotropic	sample_conditions_1
3D HN(CA)CO	sample_2	isotropic	sample_conditions_1
3D H(CCO)NH	sample_2	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D H(CCO)NH	sample_2	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D HNHA	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_4	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_4	isotropic	sample_conditions_1
4D HCCH NOESY	sample_4	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_5	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_3	isotropic	sample_conditions_1
2D DQF-COSY	sample_3	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_3	isotropic	sample_conditions_1

Software:

NMRPipe v2.5, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - data analysis, processing

CARA v1.5.5, Rochus Keller & Datonal AG - chemical shift assignment

X-PLOR NIH v2.11.2, Schwieters, Kuszewski, Tjandra and Clore - structure solution

NMR spectrometers:

Bruker DRX 500 MHz
Bruker DMX 600 MHz
Bruker Avance 800 MHz
Bruker Avance 900 MHz

PDB	2JMP
GB	AAC72490 ABY79668 AFQ03308 AFQ03792 AFQ04301
REF	WP_010869493 WP_014894707
SP	P35888
AlphaFold	P35888

1	MET	GLU	GLN	PHE	ASN	ALA	PHE	LYS	SER	LEU
2	LEU	LYS	LYS	HIS	TYR	GLU	LYS	THR	ILE	GLY
3	PHE	HIS	ASP	LYS	TYR	ILE	LYS	ASP	ILE	ASN
4	ARG	PHE	VAL	PHE	LYS	ASN	ASN	VAL	LEU	LEU
5	ILE	LEU	LEU	GLU	ASN	GLU	PHE	ALA	ARG	ASN
6	SER	LEU	ASN	ASP	ASN	SER	GLU	ILE	ILE	HIS
7	LEU	ALA	GLU	SER	LEU	TYR	GLU	GLY	ILE	LYS
8	SER	VAL	ASN	PHE	VAL	ASN	GLU	GLN	ASP	PHE
9	PHE	PHE	ASN	LEU	ALA	LYS	LEU	GLU	GLU	ASN
10	SER	ARG	ASP	THR	LEU	TYR	GLN	ASN	SER	GLY

1	MET	GLU	GLN	PHE	ASN	ALA	PHE	LYS	SER	LEU
2	LEU	LYS	LYS	HIS	TYR	GLU	LYS	THR	ILE	GLY
3	PHE	HIS	ASP	LYS	TYR	ILE	LYS	ASP	ILE	ASN
4	ARG	PHE	VAL	PHE	LYS	ASN	ASN	VAL	LEU	LEU
5	ILE	LEU	LEU	GLU	ASN	GLU	PHE	ALA	ARG	ASN
6	SER	LEU	ASN	ASP	ASN	SER	GLU	ILE	ILE	HIS
7	LEU	ALA	GLU	SER	LEU	TYR	GLU	GLY	ILE	LYS
8	SER	VAL	ASN	PHE	VAL	ASN	GLU	GLN	ASP	PHE
9	PHE	PHE	ASN	LEU	ALA	LYS	LEU	GLU	GLU	ASN
10	SER	ARG	ASP	THR	LEU	TYR	GLN	ASN	SER	GLY