BMRB Entry 11422

Name: Solution structure of the E. coli ORF135 protein
Published: 2013-02-07

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PDB ID: 2rrk
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR11422
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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:

Solution structure of the E. coli ORF135 protein

Deposition date:

2011-01-01

Original release date:

2013-02-07

Authors:

Kawasaki, Kumiko; Mishima, Masaki

Citation:

Citation: Kawasaki, Kumiko; Yoneyama, Momoko; Murata-Kamiya, Naoko; Harashima, Hideyoshi; Kojima, Chojiro; Ito, Yutaka; Kamiya, Hiroyuki; Mishima, Masaki. "(1)H, (13)C and (15)N NMR assignments of the Escherichia coli Orf135 protein." Biomol. NMR Assignments ., .-. (2011).
PubMed: 21553121

Assembly members:

Assembly members:
ORF135 protein, polymer, 140 residues, 15476.681 Da.

Natural source:

Natural source: Common Name: E. coli Taxonomy ID: 83333 Superkingdom: Eubacteria Kingdom: not available Genus/species: Escherichia coli

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pGEX6P3

Entity Sequences (FASTA):

Entity Sequences (FASTA):
ORF135 protein: GPLGSMKMIEVVAAIIERDG KILLAQRPAQSDQAGLWEFA GGKVEPDESQRQALVRELRE ELGIEATVGEYVASHQREVS GRIIHLHAWHVPDFHGTLQA HEHQALVWCSPEEALQYPLA PADIPLLEAFMALRAARPAD

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	557
15N chemical shifts	132
1H chemical shifts	879

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	ORF135 protein	1

Entities:

Entity 1, ORF135 protein 140 residues - 15476.681 Da.

1	GLY	PRO	LEU	GLY	SER	MET	LYS	MET	ILE	GLU
2	VAL	VAL	ALA	ALA	ILE	ILE	GLU	ARG	ASP	GLY
3	LYS	ILE	LEU	LEU	ALA	GLN	ARG	PRO	ALA	GLN
4	SER	ASP	GLN	ALA	GLY	LEU	TRP	GLU	PHE	ALA
5	GLY	GLY	LYS	VAL	GLU	PRO	ASP	GLU	SER	GLN
6	ARG	GLN	ALA	LEU	VAL	ARG	GLU	LEU	ARG	GLU
7	GLU	LEU	GLY	ILE	GLU	ALA	THR	VAL	GLY	GLU
8	TYR	VAL	ALA	SER	HIS	GLN	ARG	GLU	VAL	SER
9	GLY	ARG	ILE	ILE	HIS	LEU	HIS	ALA	TRP	HIS
10	VAL	PRO	ASP	PHE	HIS	GLY	THR	LEU	GLN	ALA
11	HIS	GLU	HIS	GLN	ALA	LEU	VAL	TRP	CYS	SER
12	PRO	GLU	GLU	ALA	LEU	GLN	TYR	PRO	LEU	ALA
13	PRO	ALA	ASP	ILE	PRO	LEU	LEU	GLU	ALA	PHE
14	MET	ALA	LEU	ARG	ALA	ALA	ARG	PRO	ALA	ASP

Samples:

sample_1: ORF135 protein, [U-99% 15N], 1 mM; potassium phosphate 50 mM; potassium chloride 20 mM; DTT 1 mM; EDTA 0.1 mM; H2O 93%; D2O 7%

sample_2: ORF135 protein, [U-99% 13C; U-99% 15N], 1 mM; potassium phosphate 50 mM; potassium chloride 20 mM; DTT 1 mM; EDTA 0.1 mM; H2O 93%; D2O 7%

sample_3: ORF135 protein, [U-99% 13C; U-99% 15N], 1 mM; potassium phosphate 50 mM; potassium chloride 20 mM; DTT 1 mM; EDTA 0.1 mM; D2O 100%

sample_conditions_1: ionic strength: 70 mM; pH: 6.9; pressure: 1 atm; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_2	isotropic	sample_conditions_1
3D HN(CO)CACB	sample_2	isotropic	sample_conditions_1
3D HN(CA)CO	sample_2	isotropic	sample_conditions_1
3D HNCO	sample_2	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_3	isotropic	sample_conditions_1
3D H(CCO)NH	sample_2	isotropic	sample_conditions_1
3D C(CO)NH	sample_2	isotropic	sample_conditions_1
4D HC(CO)NH	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_3	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
2D 15N filtered NOESY	sample_1	isotropic	sample_conditions_1
3D HNHA	sample_1	isotropic	sample_conditions_1

Software:

xwinnmr, Bruker Biospin - collection

TOPSPIN, Bruker Biospin - collection

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

TALOS, Cornilescu, Delaglio and Bax - data analysis

SPARKY, Goddard - chemical shift assignment, data analysis, peak picking

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

NMR spectrometers:

Bruker Avance 500 MHz
Bruker Avance 600 MHz
Bruker DRX 800 MHz

PDB	2RRK
DBJ	BAA15549 BAB35888 BAG77454 BAI25775 BAI30753
EMBL	CAP76253 CAQ32233 CAQ98676 CAR03119 CAR13244
GB	AAC74829 AAG56745 ABB61654 ABE07431 ABG69708
REF	NP_310492 NP_416273 WP_000296338 WP_000781861 WP_000781866
SP	P77788
AlphaFold	P77788

1	GLY	PRO	LEU	GLY	SER	MET	LYS	MET	ILE	GLU
2	VAL	VAL	ALA	ALA	ILE	ILE	GLU	ARG	ASP	GLY
3	LYS	ILE	LEU	LEU	ALA	GLN	ARG	PRO	ALA	GLN
4	SER	ASP	GLN	ALA	GLY	LEU	TRP	GLU	PHE	ALA
5	GLY	GLY	LYS	VAL	GLU	PRO	ASP	GLU	SER	GLN
6	ARG	GLN	ALA	LEU	VAL	ARG	GLU	LEU	ARG	GLU
7	GLU	LEU	GLY	ILE	GLU	ALA	THR	VAL	GLY	GLU
8	TYR	VAL	ALA	SER	HIS	GLN	ARG	GLU	VAL	SER
9	GLY	ARG	ILE	ILE	HIS	LEU	HIS	ALA	TRP	HIS
10	VAL	PRO	ASP	PHE	HIS	GLY	THR	LEU	GLN	ALA
11	HIS	GLU	HIS	GLN	ALA	LEU	VAL	TRP	CYS	SER
12	PRO	GLU	GLU	ALA	LEU	GLN	TYR	PRO	LEU	ALA
13	PRO	ALA	ASP	ILE	PRO	LEU	LEU	GLU	ALA	PHE
14	MET	ALA	LEU	ARG	ALA	ALA	ARG	PRO	ALA	ASP

1	GLY	PRO	LEU	GLY	SER	MET	LYS	MET	ILE	GLU
2	VAL	VAL	ALA	ALA	ILE	ILE	GLU	ARG	ASP	GLY
3	LYS	ILE	LEU	LEU	ALA	GLN	ARG	PRO	ALA	GLN
4	SER	ASP	GLN	ALA	GLY	LEU	TRP	GLU	PHE	ALA
5	GLY	GLY	LYS	VAL	GLU	PRO	ASP	GLU	SER	GLN
6	ARG	GLN	ALA	LEU	VAL	ARG	GLU	LEU	ARG	GLU
7	GLU	LEU	GLY	ILE	GLU	ALA	THR	VAL	GLY	GLU
8	TYR	VAL	ALA	SER	HIS	GLN	ARG	GLU	VAL	SER
9	GLY	ARG	ILE	ILE	HIS	LEU	HIS	ALA	TRP	HIS
10	VAL	PRO	ASP	PHE	HIS	GLY	THR	LEU	GLN	ALA
11	HIS	GLU	HIS	GLN	ALA	LEU	VAL	TRP	CYS	SER
12	PRO	GLU	GLU	ALA	LEU	GLN	TYR	PRO	LEU	ALA
13	PRO	ALA	ASP	ILE	PRO	LEU	LEU	GLU	ALA	PHE
14	MET	ALA	LEU	ARG	ALA	ALA	ARG	PRO	ALA	ASP