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BMRB: 15211

2JOZ

Solution NMR structure of protein , Northeastprotein yxeF Structural Genomics Consortium target Sr500a

Authors

Wu, Y., Liu, G., Zhang, Q., Bhatnagar, S., Chen, C., Nwosu, C., Xiao, R., Cunningham, K., Locke, J., Ma, L., Swapna, G., Baran, M., Acton, T., Montelione, G., Szyperski, T.

Assembly

protein yxeF

Entity

1. protein yxeF (polymer, Thiol state: all free), 135 monomers, 15421.97 Da Detail

MIMVSGCQQQ KEETPFYYGT WDEGRAPGPT DGVKSATVTF TEDEVVETEV MEGRGEVQLP FMAYKVISQS TDGSIEIQYL GPYYPLKSTL KRGENGTLIW EQNGQRKTMT RIESKTGREE KDEKSKSLEH HHHHH

Formula weight

15421.97 Da

Source organism

Bacillus subtilis

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.8 %, Completeness: 92.0 %, Completeness (bb): 93.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	92.0 % (1447 of 1572)	93.4 % (770 of 824)	89.8 % (545 of 607)	93.6 % (132 of 141)
Backbone	93.9 % (749 of 798)	94.6 % (262 of 277)	93.1 % (365 of 392)	94.6 % (122 of 129)
Sidechain	90.7 % (813 of 896)	92.9 % (508 of 547)	87.5 % (295 of 337)	83.3 % (10 of 12)
Aromatic	67.5 % (85 of 126)	81.0 % (51 of 63)	52.5 % (32 of 61)	100.0 % (2 of 2)
Methyl	100.0 % (112 of 112)	100.0 % (56 of 56)	100.0 % (56 of 56)

1. protein yxeF

MIMVSGCQQQ KEETPFYYGT WDEGRAPGPT DGVKSATVTF TEDEVVETEV MEGRGEVQLP FMAYKVISQS TDGSIEIQYL GPYYPLKSTL KRGENGTLIW EQNGQRKTMT RIESKTGREE KDEKSKSLEH HHHHH

Show sample condition

Sample #1

Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1mM protein Sr500a, 10mM Tris, 100mM NaCl, 0.02% NaN3

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	1 mM
2	Tris		10 mM
3	NaCl		100 %
4	NaN3		0.02 %

Sample #2

Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1mM protein Sr500a, 10mM Tris, 100mM NaCl, 0.02% NaN3

#	Name	Isotope labeling	Concentration
5	entity	[U-10% 13C; U-100% 15N]	1 mM
6	Tris		10 mM
7	NaCl		100 %
8	NaN3		0.02 %

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: -0.12 ppm, Outliers: 2 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: -0.12 ppm, Outliers: 2 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: -0.09 ppm, Outliers: 2 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: 0.26 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2007-06-04

Citation

Solution NMR structure of protein, Northeastprotein yxeF Structural Genomics Consortium target Sr500a
Wu, Y., Liu, G., Zhang, Q., Bhatnagar, S., Chen, C., Nwosu, C., Xiao, R., Cunningham, K., Locke, J., Ma, L., Swapna, G., Baran, M., Acton, T., Montelione, G., Szyperski, T.
Protein Sci.

Related entities 1. protein yxeF, : 1 : 1 entities Detail

Experiments performed 6 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15211_2joz.nef
Input source #2: Coordindates	2joz.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-------100
MIMVSGCQQQKEETPFYYGTWDEGRAPGPTDGVKSATVTFTEDEVVETEVMEGRGEVQLPFMAYKVISQSTDGSIEIQYLGPYYPLKSTLKRGENGTLIW
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MIMVSGCQQQKEETPFYYGTWDEGRAPGPTDGVKSATVTFTEDEVVETEVMEGRGEVQLPFMAYKVISQSTDGSIEIQYLGPYYPLKSTLKRGENGTLIW

-------110-------120-------130-----
EQNGQRKTMTRIESKTGREEKDEKSKSLEHHHHHH
|||||||||||||||||||||||||||||||||||
EQNGQRKTMTRIESKTGREEKDEKSKSLEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	135	0	0	100.0

Content subtype: combined_15211_2joz.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1447		94.8 (chain: A, length: 135)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	2084 (1)	noe	91.1 (chain: A, length: 135)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	249 (249)	.	79.3 (chain: A, length: 135)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 135, Sequence coverage: 94.8%
- Total number of assignments
  - ¹H chemical shifts: 774
  - ¹³C chemical shifts: 542
  - ¹⁵N chemical shifts: 131
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
64	TYR	HH	9.5
79	TYR	HH	9.34
88	SER	HG	3.86

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	824	771	93.6
¹³C chemical shifts	607	542	89.3
¹⁵N chemical shifts	147	131	89.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	277	263	94.9
¹³C chemical shifts	270	249	92.2
¹⁵N chemical shifts	129	122	94.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	547	508	92.9
¹³C chemical shifts	337	293	86.9
¹⁵N chemical shifts	18	9	50.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	61	56	91.8
¹³C chemical shifts	61	56	91.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	63	51	81.0
¹³C chemical shifts	61	30	49.2
¹⁵N chemical shifts	2	2	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 135, Sequence coverage: 91.1%
- Total number of restraints: 2084
- Weight of restraints: 1.0 (2084)
- Potential type of restraints: square-well-parabolic (2084)
- Range of distance target values: 2.1, 5.39 (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

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 135, Sequence coverage: 79.3%
- Total number of restraints: 249
- Total number of restraints per polymer type: 249
- Weight of restraints: 1.0 (249)
- Potential type of restraints: square-well-parabolic (249)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

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Found 1 Document (0.603 seconds)

BMRB: 15211

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. protein yxeF, : 1 : 1 entities Detail

Experiments performed 6 experiments Detail

Instrument

Sample

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Sample

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NMR combined restraints 4 contents Detail