BMRBj - BMREntryMaster

Found 1 Document (0.549 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

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.549 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

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail