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Found 1 Document (0.615 seconds)

BMRB: 15190

2JOQ

Solution Structure of Protein HP0495 from H. pylori; Northeast structural genomics consortium target PT2; Ontario Centre for Structural Proteomics target HP0488

Authors

Gutmanas, A., Lemak, A., Yee, A., Karra, M., Srisailam, S., Semesi, A., Arrowsmith, C.H.

Assembly

HP0495

Entity

1. HP0495 (polymer, Thiol state: all free), 91 monomers, 10659.03 Da Detail

QGHMPSDSKK PTIIYPCLWD YRVIMTTKDT STLKELLETY QRPFKLEFKN TSKNAKFYSF NVSMEVSNES ERNEIFQKIS QLDKVVQTLG S

Formula weight

10659.03 Da

Source organism

Helicobacter pylori

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 98.9 %, Completeness: 95.6 %, Completeness (bb): 95.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	95.6 % (1074 of 1124)	95.8 % (566 of 591)	95.4 % (415 of 435)	94.9 % (93 of 98)
Backbone	95.5 % (514 of 538)	97.2 % (175 of 180)	94.5 % (256 of 271)	95.4 % (83 of 87)
Sidechain	95.7 % (646 of 675)	95.1 % (391 of 411)	96.8 % (245 of 253)	90.9 % (10 of 11)
Aromatic	100.0 % (98 of 98)	100.0 % (49 of 49)	100.0 % (48 of 48)	100.0 % (1 of 1)
Methyl	100.0 % (86 of 86)	100.0 % (43 of 43)	100.0 % (43 of 43)

1. HP0495

QGHMPSDSKK PTIIYPCLWD YRVIMTTKDT STLKELLETY QRPFKLEFKN TSKNAKFYSF NVSMEVSNES ERNEIFQKIS QLDKVVQTLG S

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.5 mM HP0495, U-15N,13C; 10 mM tris, 300 mM NaCl, 1 mM benzamidine, 10 mM DTT, 0.01% NaN3, pH 7.0, 95% H2O, 5% D2O

#	Name	Isotope labeling	Concentration
1	HP0495	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride	natural abundance	300 mM
4	benzamidine	natural abundance	1 mM
5	DTT	natural abundance	10 mM
6	sodium azide	natural abundance	0.01 %
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.5 mM HP0495, U-15N,13C; 10 mM tris, 300 mM NaCl, 1 mM benzamidine, 10 mM DTT, 0.01% NaN3, pH 7.0, 95% H2O, 5% D2O

#	Name	Isotope labeling	Concentration
9	HP0495	[U-13C; U-15N]	0.5 mM
10	TRIS	natural abundance	10 mM
11	sodium chloride	natural abundance	300 mM
12	benzamidine	natural abundance	1 mM
13	DTT	natural abundance	10 mM
14	sodium azide	natural abundance	0.01 %
15	D2O	natural abundance	100 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.16 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.16 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: 0.0 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: 3.15 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2JOQ, Strand ID: A Detail

Release date

2009-06-14

Citation

Solution Structure of Protein HP0495 from H. pylori
Gutmanas, A., Lemak, A., Yee, A., Karra, M., Srisailam, S., Semesi, A., Arrowsmith, C.H.
Not known

Related entities 1. HP0495, : 1 : 2 : 2 entities Detail

Interaction partners 1. HP0495, : 7 interactors Detail

More details for 7 interactors identified by 2 citations

Experiments performed 19 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.5 mM HP0495, U-15N,13C; 10 mM tris, 300 mM NaCl, 1 mM benzamidine, 10 mM DTT, 0.01% NaN3, pH 7.0, 95% H2O, 5% D2O

#	Name	Isotope labeling	Concentration
1	HP0495	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride	natural abundance	300 mM
4	benzamidine	natural abundance	1 mM
5	DTT	natural abundance	10 mM
6	sodium azide	natural abundance	0.01 %
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	HP0495	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride	natural abundance	300 mM
4	benzamidine	natural abundance	1 mM
5	DTT	natural abundance	10 mM
6	sodium azide	natural abundance	0.01 %
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	HP0495	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride	natural abundance	300 mM
4	benzamidine	natural abundance	1 mM
5	DTT	natural abundance	10 mM
6	sodium azide	natural abundance	0.01 %
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

4 3D HNCO sparse

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	HP0495	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride	natural abundance	300 mM
4	benzamidine	natural abundance	1 mM
5	DTT	natural abundance	10 mM
6	sodium azide	natural abundance	0.01 %
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

5 3D HNCA sparse

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	HP0495	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride	natural abundance	300 mM
4	benzamidine	natural abundance	1 mM
5	DTT	natural abundance	10 mM
6	sodium azide	natural abundance	0.01 %
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

6 3D H(CCCO)NH-TOCSY sparse

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	HP0495	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride	natural abundance	300 mM
4	benzamidine	natural abundance	1 mM
5	DTT	natural abundance	10 mM
6	sodium azide	natural abundance	0.01 %
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

7 3D (H)C(CCO)NH-TOCSY

Instrument

Varian INOVA - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	HP0495	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride	natural abundance	300 mM
4	benzamidine	natural abundance	1 mM
5	DTT	natural abundance	10 mM
6	sodium azide	natural abundance	0.01 %
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

8 4D HBHACBCA(CO)NH PR

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	HP0495	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride	natural abundance	300 mM
4	benzamidine	natural abundance	1 mM
5	DTT	natural abundance	10 mM
6	sodium azide	natural abundance	0.01 %
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

9 4D HC(CCO)NH-TOCSY PR

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	HP0495	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride	natural abundance	300 mM
4	benzamidine	natural abundance	1 mM
5	DTT	natural abundance	10 mM
6	sodium azide	natural abundance	0.01 %
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

10 3D 1H-15N NOESY sparse

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	HP0495	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride	natural abundance	300 mM
4	benzamidine	natural abundance	1 mM
5	DTT	natural abundance	10 mM
6	sodium azide	natural abundance	0.01 %
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

11 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	HP0495	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride	natural abundance	300 mM
4	benzamidine	natural abundance	1 mM
5	DTT	natural abundance	10 mM
6	sodium azide	natural abundance	0.01 %
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

12 3D H(C)CH-TOCSY sparse

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.5 mM HP0495, U-15N,13C; 10 mM tris, 300 mM NaCl, 1 mM benzamidine, 10 mM DTT, 0.01% NaN3, pH 7.0, 95% H2O, 5% D2O

#	Name	Isotope labeling	Concentration
9	HP0495	[U-13C; U-15N]	0.5 mM
10	TRIS	natural abundance	10 mM
11	sodium chloride	natural abundance	300 mM
12	benzamidine	natural abundance	1 mM
13	DTT	natural abundance	10 mM
14	sodium azide	natural abundance	0.01 %
15	D2O	natural abundance	100 %

13 3D (H)CCH-TOCSY sparse

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
9	HP0495	[U-13C; U-15N]	0.5 mM
10	TRIS	natural abundance	10 mM
11	sodium chloride	natural abundance	300 mM
12	benzamidine	natural abundance	1 mM
13	DTT	natural abundance	10 mM
14	sodium azide	natural abundance	0.01 %
15	D2O	natural abundance	100 %

14 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	HP0495	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride	natural abundance	300 mM
4	benzamidine	natural abundance	1 mM
5	DTT	natural abundance	10 mM
6	sodium azide	natural abundance	0.01 %
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

15 3D 1H-13C NOESY sparse

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
9	HP0495	[U-13C; U-15N]	0.5 mM
10	TRIS	natural abundance	10 mM
11	sodium chloride	natural abundance	300 mM
12	benzamidine	natural abundance	1 mM
13	DTT	natural abundance	10 mM
14	sodium azide	natural abundance	0.01 %
15	D2O	natural abundance	100 %

16 3D H(C)CH-TOCSY aromatic, sparse

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
9	HP0495	[U-13C; U-15N]	0.5 mM
10	TRIS	natural abundance	10 mM
11	sodium chloride	natural abundance	300 mM
12	benzamidine	natural abundance	1 mM
13	DTT	natural abundance	10 mM
14	sodium azide	natural abundance	0.01 %
15	D2O	natural abundance	100 %

17 3D (H)CCH-TOCSY aromatic

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
9	HP0495	[U-13C; U-15N]	0.5 mM
10	TRIS	natural abundance	10 mM
11	sodium chloride	natural abundance	300 mM
12	benzamidine	natural abundance	1 mM
13	DTT	natural abundance	10 mM
14	sodium azide	natural abundance	0.01 %
15	D2O	natural abundance	100 %

18 2D CT 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
9	HP0495	[U-13C; U-15N]	0.5 mM
10	TRIS	natural abundance	10 mM
11	sodium chloride	natural abundance	300 mM
12	benzamidine	natural abundance	1 mM
13	DTT	natural abundance	10 mM
14	sodium azide	natural abundance	0.01 %
15	D2O	natural abundance	100 %

19 2D CT 1H-13C HSQC aromatic

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
9	HP0495	[U-13C; U-15N]	0.5 mM
10	TRIS	natural abundance	10 mM
11	sodium chloride	natural abundance	300 mM
12	benzamidine	natural abundance	1 mM
13	DTT	natural abundance	10 mM
14	sodium azide	natural abundance	0.01 %
15	D2O	natural abundance	100 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15190_2joq.nef
Input source #2: Coordindates	2joq.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--------80--------90-
QGHMPSDSKKPTIIYPCLWDYRVIMTTKDTSTLKELLETYQRPFKLEFKNTSKNAKFYSFNVSMEVSNESERNEIFQKISQLDKVVQTLGS
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
QGHMPSDSKKPTIIYPCLWDYRVIMTTKDTSTLKELLETYQRPFKLEFKNTSKNAKFYSFNVSMEVSNESERNEIFQKISQLDKVVQTLGS

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	91	0	0	100.0

Content subtype: combined_15190_2joq.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1065		97.8 (chain: A, length: 91)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	2859 (1)	noe	95.6 (chain: A, length: 91)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	4 (1)	hbond	4.4 (chain: A, length: 91)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	106 (106)	.	82.4 (chain: A, length: 91)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 91, Sequence coverage: 97.8%
- Total number of assignments
  - ¹H chemical shifts: 561
  - ¹³C chemical shifts: 413
  - ¹⁵N chemical shifts: 91
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
56	LYS	HZ1	6.031
56	LYS	HZ2	6.031
56	LYS	HZ3	6.031
56	LYS	NZ	109.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	591	558	94.4
¹³C chemical shifts	435	413	94.9
¹⁵N chemical shifts	101	90	89.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	180	170	94.4
¹³C chemical shifts	182	168	92.3
¹⁵N chemical shifts	87	80	92.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	411	388	94.4
¹³C chemical shifts	253	245	96.8
¹⁵N chemical shifts	14	10	71.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	46	46	100.0
¹³C chemical shifts	46	46	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	49	49	100.0
¹³C chemical shifts	48	48	100.0
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 91, Sequence coverage: 95.6%
- Total number of restraints: 2858
- Weight of restraints: 1.0 (2858)
- Potential type of restraints: square-well-parabolic (2858)
- 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
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 91, Sequence coverage: 4.4%
  - Total number of restraints: 4
  - Weight of restraints: 1.0 (4)
  - Potential type of restraints: square-well-parabolic (4)
  - Range of distance target values: 2.05, 3.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 91, Sequence coverage: 82.4%
- Total number of restraints: 106
- Total number of restraints per polymer type: 106
- Weight of restraints: 1.0 (106)
- Potential type of restraints: square-well-parabolic (106)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords ABACUS, HP0495, non-uniform sampling, structural genomics

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Found 1 Document (0.615 seconds)

BMRB: 15190

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. HP0495, : 1 : 2 : 2 entities Detail

Interaction partners 1. HP0495, : 7 interactors Detail

Experiments performed 19 experiments Detail

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NMR combined restraints 5 contents Detail