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Found 1 Document (0.573 seconds)

BMRB: 30348

6B3N

Solution structure of the N-terminal domain of the effector NleG5-1 from Escherichia coli O157:H7 str. Sakai

Authors

Valleau, D., Houliston, S., Lemak, A., Anderson, W.F., Arrowsmith, C., Savchenko, A., Center for Structural Genomics of Infectious Diseases (CSGID), C.

Assembly

NleG5-1

Entity

1. NleG5-1 (polymer, Thiol state: not present), 137 monomers, 15660.42 Da Detail

MGSSHHHHHH SSGRENLYFQ GMPVDLTPYI LPGVSFLSDI PQETLSEIRN QTIRGEAQIR LGELMVSIRP MQVNGYFMGS LNQDGLSNDN IQIGLQYIEH IERTLNHGSL TSREVTVLRE IEMLENMDLL SNYQLEE

Formula weight

15660.42 Da

Source organism

Escherichia coli O157:H7

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 87.6 %, Completeness: 76.2 %, Completeness (bb): 81.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	76.2 % (1218 of 1598)	76.2 % (635 of 833)	76.6 % (471 of 615)	74.7 % (112 of 150)
Backbone	81.4 % (661 of 812)	82.9 % (232 of 280)	79.8 % (319 of 400)	83.3 % (110 of 132)
Sidechain	72.3 % (659 of 912)	72.9 % (403 of 553)	74.5 % (254 of 341)	11.1 % (2 of 18)
Aromatic	47.1 % (48 of 102)	58.8 % (30 of 51)	35.3 % (18 of 51)
Methyl	93.3 % (140 of 150)	94.7 % (71 of 75)	92.0 % (69 of 75)

1. entity 1

MGSSHHHHHH SSGRENLYFQ GMPVDLTPYI LPGVSFLSDI PQETLSEIRN QTIRGEAQIR LGELMVSIRP MQVNGYFMGS LNQDGLSNDN IQIGLQYIEH IERTLNHGSL TSREVTVLRE IEMLENMDLL SNYQLEE

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5, Details 400 uM [U-100% 13C; U-100% 15N] NleG5-1, 15 mM HEPES, 250 mM sodium chloride, 5 mM L-arginine, 5 mM sodium citrate, 1 mM benzamidine, 10 uM DTT, 0.01 % w/v sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	10 uM
2	HEPES	natural abundance	15 mM
3	L-arginine	natural abundance	5 mM
4	NleG5-1	[U-100% 13C; U-100% 15N]	400 uM
5	benzamidine	natural abundance	1 mM
6	sodium azide	natural abundance	0.01 % w/v
7	sodium chloride	natural abundance	250 mM
8	sodium citrate	natural abundance	5 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.251
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.101

Referencing offset: 0.07 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.251
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.101

Referencing offset: 0.07 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.251
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.101

Referencing offset: -0.04 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.251
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.101

Referencing offset: 0.0 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 6B3N, Strand ID: A Detail

Release date

2017-10-31

Citation

Solution structure of the N-terminal domain of the effector NleG5-1 from Escherichia coli O157:H7 str. Sakai
Valleau, D., Savchenko, A.

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5, Details 400 uM [U-100% 13C; U-100% 15N] NleG5-1, 15 mM HEPES, 250 mM sodium chloride, 5 mM L-arginine, 5 mM sodium citrate, 1 mM benzamidine, 10 uM DTT, 0.01 % w/v sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	10 uM
2	HEPES	natural abundance	15 mM
3	L-arginine	natural abundance	5 mM
4	NleG5-1	[U-100% 13C; U-100% 15N]	400 uM
5	benzamidine	natural abundance	1 mM
6	sodium azide	natural abundance	0.01 % w/v
7	sodium chloride	natural abundance	250 mM
8	sodium citrate	natural abundance	5 mM

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	10 uM
2	HEPES	natural abundance	15 mM
3	L-arginine	natural abundance	5 mM
4	NleG5-1	[U-100% 13C; U-100% 15N]	400 uM
5	benzamidine	natural abundance	1 mM
6	sodium azide	natural abundance	0.01 % w/v
7	sodium chloride	natural abundance	250 mM
8	sodium citrate	natural abundance	5 mM

3 3D HNCA

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	10 uM
2	HEPES	natural abundance	15 mM
3	L-arginine	natural abundance	5 mM
4	NleG5-1	[U-100% 13C; U-100% 15N]	400 uM
5	benzamidine	natural abundance	1 mM
6	sodium azide	natural abundance	0.01 % w/v
7	sodium chloride	natural abundance	250 mM
8	sodium citrate	natural abundance	5 mM

4 3D HNCO

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	10 uM
2	HEPES	natural abundance	15 mM
3	L-arginine	natural abundance	5 mM
4	NleG5-1	[U-100% 13C; U-100% 15N]	400 uM
5	benzamidine	natural abundance	1 mM
6	sodium azide	natural abundance	0.01 % w/v
7	sodium chloride	natural abundance	250 mM
8	sodium citrate	natural abundance	5 mM

5 3D CBCA(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	10 uM
2	HEPES	natural abundance	15 mM
3	L-arginine	natural abundance	5 mM
4	NleG5-1	[U-100% 13C; U-100% 15N]	400 uM
5	benzamidine	natural abundance	1 mM
6	sodium azide	natural abundance	0.01 % w/v
7	sodium chloride	natural abundance	250 mM
8	sodium citrate	natural abundance	5 mM

6 3D 1H-15N NOESY

Instrument

Bruker AvanceII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	10 uM
2	HEPES	natural abundance	15 mM
3	L-arginine	natural abundance	5 mM
4	NleG5-1	[U-100% 13C; U-100% 15N]	400 uM
5	benzamidine	natural abundance	1 mM
6	sodium azide	natural abundance	0.01 % w/v
7	sodium chloride	natural abundance	250 mM
8	sodium citrate	natural abundance	5 mM

7 3D 1H-13C NOESY aromatic

Instrument

Bruker AvanceII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	10 uM
2	HEPES	natural abundance	15 mM
3	L-arginine	natural abundance	5 mM
4	NleG5-1	[U-100% 13C; U-100% 15N]	400 uM
5	benzamidine	natural abundance	1 mM
6	sodium azide	natural abundance	0.01 % w/v
7	sodium chloride	natural abundance	250 mM
8	sodium citrate	natural abundance	5 mM

8 3D 1H-13C NOESY aliphatic

Instrument

Bruker AvanceII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	10 uM
2	HEPES	natural abundance	15 mM
3	L-arginine	natural abundance	5 mM
4	NleG5-1	[U-100% 13C; U-100% 15N]	400 uM
5	benzamidine	natural abundance	1 mM
6	sodium azide	natural abundance	0.01 % w/v
7	sodium chloride	natural abundance	250 mM
8	sodium citrate	natural abundance	5 mM

9 3D HBHA(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	10 uM
2	HEPES	natural abundance	15 mM
3	L-arginine	natural abundance	5 mM
4	NleG5-1	[U-100% 13C; U-100% 15N]	400 uM
5	benzamidine	natural abundance	1 mM
6	sodium azide	natural abundance	0.01 % w/v
7	sodium chloride	natural abundance	250 mM
8	sodium citrate	natural abundance	5 mM

10 3D HCCH-TOCSY

Instrument

Bruker AvanceII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	10 uM
2	HEPES	natural abundance	15 mM
3	L-arginine	natural abundance	5 mM
4	NleG5-1	[U-100% 13C; U-100% 15N]	400 uM
5	benzamidine	natural abundance	1 mM
6	sodium azide	natural abundance	0.01 % w/v
7	sodium chloride	natural abundance	250 mM
8	sodium citrate	natural abundance	5 mM

11 3D CCH-TOCSY

Instrument

Bruker AvanceII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	10 uM
2	HEPES	natural abundance	15 mM
3	L-arginine	natural abundance	5 mM
4	NleG5-1	[U-100% 13C; U-100% 15N]	400 uM
5	benzamidine	natural abundance	1 mM
6	sodium azide	natural abundance	0.01 % w/v
7	sodium chloride	natural abundance	250 mM
8	sodium citrate	natural abundance	5 mM

12 3D 1H-13C NOESY aromatic

Instrument

Bruker AvanceII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	10 uM
2	HEPES	natural abundance	15 mM
3	L-arginine	natural abundance	5 mM
4	NleG5-1	[U-100% 13C; U-100% 15N]	400 uM
5	benzamidine	natural abundance	1 mM
6	sodium azide	natural abundance	0.01 % w/v
7	sodium chloride	natural abundance	250 mM
8	sodium citrate	natural abundance	5 mM

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_30348_6b3n.nef
Input source #2: Coordindates	6b3n.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

-----------------------------10--------20--------30--------40--------50--------60--------70--------8
MGSSHHHHHHSSGRENLYFQGMPVDLTPYILPGVSFLSDIPQETLSEIRNQTIRGEAQIRLGELMVSIRPMQVNGYFMGSLNQDGLSNDNIQIGLQYIEH
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGSSHHHHHHSSGRENLYFQGMPVDLTPYILPGVSFLSDIPQETLSEIRNQTIRGEAQIRLGELMVSIRPMQVNGYFMGSLNQDGLSNDNIQIGLQYIEH
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

0--------90-------100-------110------
IERTLNHGSLTSREVTVLREIEMLENMDLLSNYQLEE
|||||||||||||||||||||||||||||||||||||
IERTLNHGSLTSREVTVLREIEMLENMDLLSNYQLEE
-------110-------120-------130-------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	137	0	0	100.0

Content subtype: combined_30348_6b3n.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1116		83.2 (chain: A, length: 137)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	2564 (1)	noe	68.6 (chain: A, length: 137)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 137, Sequence coverage: 83.2%
- Total number of assignments
  - ¹H chemical shifts: 581
  - ¹⁵N chemical shifts: 97
  - ¹³C chemical shifts: 438
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	833	581	69.7
¹⁵N chemical shifts	158	97	61.4
¹³C chemical shifts	615	438	71.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	280	214	76.4
¹⁵N chemical shifts	132	97	73.5
¹³C chemical shifts	274	204	74.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	553	367	66.4
¹⁵N chemical shifts	26	0	0.0
¹³C chemical shifts	341	234	68.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	82	68	82.9
¹³C chemical shifts	82	68	82.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	51	16	31.4
¹³C chemical shifts	51	8	15.7

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 137, Sequence coverage: 68.6%
- Total number of restraints: 2564
- Weight of restraints: 1.0 (2564)
- Potential type of restraints: square-well-parabolic (2564)
- Range of distance target values: 2.25, 3.9 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Keywords Binding domain, CSGID, Center for Structural Genomics of Infectious Diseases, Effector protein, Pathogenesis, Structural Genomics

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Found 1 Document (0.573 seconds)

BMRB: 30348

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Experiments performed 12 experiments Detail

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NMR combined restraints 3 contents Detail