BMRBj - BMREntryMaster

Found 1 Document (0.788 seconds)

BMRB: 15335

2K3A

Structure of Staphylococcus saprophyticus CHAP domain protein. Northeast Structural Genomics Target SyR11.

Authors

Rossi, P., Aramini, J.M., Chen, C.X., Nwosu, C., Cunningham, K., Owens, L., Xiao, R., Liu, J., Baran, M.C., Swapna, G., Acton, T.B., Rost, B., Montelione, G.T.

Assembly

SyR11

Entity

1. SyR11 (polymer, Thiol state: all free), 163 monomers, 16980.96 Da Detail

MKKLVTATTL TAGIGAAIVG LDHGNEADAA EQTQPTNQST TQSTSGSSAN LYTAGQCTWY VYDKVGGNIG STWGNANNWA SAASSAGYTV NNSPEAGSIL QSTAGGYGHV AYVENVNSDG SVEVSEMNYN GGPFSVSERT ISAGEASSYN YIHLNLEHHH HHH

Formula weight

16980.96 Da

Source organism

Staphylococcus saprophyticus

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 96.9 %, Completeness: 93.8 %, Completeness (bb): 95.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	93.8 % (1587 of 1691)	93.7 % (797 of 851)	93.6 % (614 of 656)	95.7 % (176 of 184)
Backbone	95.8 % (931 of 972)	95.0 % (325 of 342)	96.4 % (453 of 470)	95.6 % (153 of 160)
Sidechain	91.9 % (793 of 863)	92.7 % (472 of 509)	90.3 % (298 of 330)	95.8 % (23 of 24)
Aromatic	77.9 % (120 of 154)	81.8 % (63 of 77)	73.0 % (54 of 74)	100.0 % (3 of 3)
Methyl	97.6 % (160 of 164)	97.6 % (80 of 82)	97.6 % (80 of 82)

1. SyR11

MKKLVTATTL TAGIGAAIVG LDHGNEADAA EQTQPTNQST TQSTSGSSAN LYTAGQCTWY VYDKVGGNIG STWGNANNWA SAASSAGYTV NNSPEAGSIL QSTAGGYGHV AYVENVNSDG SVEVSEMNYN GGPFSVSERT ISAGEASSYN YIHLNLEHHH HHH

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details SyR11.009

#	Name	Isotope labeling	Concentration
1	SyR11	[U-100% 13C; U-100% 15N]	0.66 mM
2	MES	natural abundance	20 mM
3	sodium azide	natural abundance	0.02 %
4	DTT	natural abundance	100 mM
5	calcium chloride	natural abundance	5 mM
6	sodium chloride	natural abundance	100 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details SyR11.006

#	Name	Isotope labeling	Concentration
7	SyR11	[U-100% 13C; U-100% 15N]	0.66 mM
8	MES	natural abundance	20 mM
9	sodium azide	natural abundance	0.02 %
10	DTT	natural abundance	100 mM
11	calcium chloride	natural abundance	5 mM
12	sodium chloride	natural abundance	100 mM

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details SyR11.004

#	Name	Isotope labeling	Concentration
13	SyR11	[U-5% 13C; U-100% 15N]	0.94 mM
14	MES	natural abundance	20 mM
15	sodium azide	natural abundance	0.02 %
16	DTT	natural abundance	100 mM
17	calcium chloride	natural abundance	5 mM
18	sodium chloride	natural abundance	100 mM

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: -0.15 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: -0.15 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: 0.02 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: 0.19 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2K3A, Strand ID: A Detail

Release date

2007-08-06

Citation

Structural elucidation of the Cys-His-Glu-Asn proteolytic relay in the secreted CHAP domain enzyme from the human pathogen Staphylococcus saprophyticus
Rossi, P., Aramini, J.M., Xiao, R., Chen, C.X., Nwosu, C., Owens, L.A., Maglaqui, M., Nair, R., Fischer, M., Acton, T.B., Honig, B., Rost, B., Montelione, G.T.
Proteins (2009), 74, 515-519, PubMed 18951393 , DOI 10.1002/prot.22267 , Abstract

Related entities 1. SyR11, : 1 : 1 entities Detail

Experiments performed 16 experiments Detail

1 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details SyR11.009

#	Name	Isotope labeling	Concentration
1	SyR11	[U-100% 13C; U-100% 15N]	0.66 mM
2	MES	natural abundance	20 mM
3	sodium azide	natural abundance	0.02 %
4	DTT	natural abundance	100 mM
5	calcium chloride	natural abundance	5 mM
6	sodium chloride	natural abundance	100 mM

2 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details SyR11.009

#	Name	Isotope labeling	Concentration
1	SyR11	[U-100% 13C; U-100% 15N]	0.66 mM
2	MES	natural abundance	20 mM
3	sodium azide	natural abundance	0.02 %
4	DTT	natural abundance	100 mM
5	calcium chloride	natural abundance	5 mM
6	sodium chloride	natural abundance	100 mM

3 3D HNCOCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details SyR11.009

#	Name	Isotope labeling	Concentration
1	SyR11	[U-100% 13C; U-100% 15N]	0.66 mM
2	MES	natural abundance	20 mM
3	sodium azide	natural abundance	0.02 %
4	DTT	natural abundance	100 mM
5	calcium chloride	natural abundance	5 mM
6	sodium chloride	natural abundance	100 mM

4 3D HBHA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details SyR11.009

#	Name	Isotope labeling	Concentration
1	SyR11	[U-100% 13C; U-100% 15N]	0.66 mM
2	MES	natural abundance	20 mM
3	sodium azide	natural abundance	0.02 %
4	DTT	natural abundance	100 mM
5	calcium chloride	natural abundance	5 mM
6	sodium chloride	natural abundance	100 mM

5 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details SyR11.009

#	Name	Isotope labeling	Concentration
1	SyR11	[U-100% 13C; U-100% 15N]	0.66 mM
2	MES	natural abundance	20 mM
3	sodium azide	natural abundance	0.02 %
4	DTT	natural abundance	100 mM
5	calcium chloride	natural abundance	5 mM
6	sodium chloride	natural abundance	100 mM

6 3D HCCH-COSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details SyR11.009

#	Name	Isotope labeling	Concentration
1	SyR11	[U-100% 13C; U-100% 15N]	0.66 mM
2	MES	natural abundance	20 mM
3	sodium azide	natural abundance	0.02 %
4	DTT	natural abundance	100 mM
5	calcium chloride	natural abundance	5 mM
6	sodium chloride	natural abundance	100 mM

7 3D CCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details SyR11.009

#	Name	Isotope labeling	Concentration
1	SyR11	[U-100% 13C; U-100% 15N]	0.66 mM
2	MES	natural abundance	20 mM
3	sodium azide	natural abundance	0.02 %
4	DTT	natural abundance	100 mM
5	calcium chloride	natural abundance	5 mM
6	sodium chloride	natural abundance	100 mM

8 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details SyR11.009

#	Name	Isotope labeling	Concentration
1	SyR11	[U-100% 13C; U-100% 15N]	0.66 mM
2	MES	natural abundance	20 mM
3	sodium azide	natural abundance	0.02 %
4	DTT	natural abundance	100 mM
5	calcium chloride	natural abundance	5 mM
6	sodium chloride	natural abundance	100 mM

9 3D 1H-13C NOESY (aliph)

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details SyR11.009

#	Name	Isotope labeling	Concentration
1	SyR11	[U-100% 13C; U-100% 15N]	0.66 mM
2	MES	natural abundance	20 mM
3	sodium azide	natural abundance	0.02 %
4	DTT	natural abundance	100 mM
5	calcium chloride	natural abundance	5 mM
6	sodium chloride	natural abundance	100 mM

10 3D 1H-13C NOESY (arom)

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details SyR11.009

#	Name	Isotope labeling	Concentration
1	SyR11	[U-100% 13C; U-100% 15N]	0.66 mM
2	MES	natural abundance	20 mM
3	sodium azide	natural abundance	0.02 %
4	DTT	natural abundance	100 mM
5	calcium chloride	natural abundance	5 mM
6	sodium chloride	natural abundance	100 mM

11 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details SyR11.006

#	Name	Isotope labeling	Concentration
7	SyR11	[U-100% 13C; U-100% 15N]	0.66 mM
8	MES	natural abundance	20 mM
9	sodium azide	natural abundance	0.02 %
10	DTT	natural abundance	100 mM
11	calcium chloride	natural abundance	5 mM
12	sodium chloride	natural abundance	100 mM

12 HETnoe

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details SyR11.004

#	Name	Isotope labeling	Concentration
13	SyR11	[U-5% 13C; U-100% 15N]	0.94 mM
14	MES	natural abundance	20 mM
15	sodium azide	natural abundance	0.02 %
16	DTT	natural abundance	100 mM
17	calcium chloride	natural abundance	5 mM
18	sodium chloride	natural abundance	100 mM

13 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details SyR11.009

#	Name	Isotope labeling	Concentration
1	SyR11	[U-100% 13C; U-100% 15N]	0.66 mM
2	MES	natural abundance	20 mM
3	sodium azide	natural abundance	0.02 %
4	DTT	natural abundance	100 mM
5	calcium chloride	natural abundance	5 mM
6	sodium chloride	natural abundance	100 mM

14 2D 1H-13C HSQC (aliph)

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details SyR11.009

#	Name	Isotope labeling	Concentration
1	SyR11	[U-100% 13C; U-100% 15N]	0.66 mM
2	MES	natural abundance	20 mM
3	sodium azide	natural abundance	0.02 %
4	DTT	natural abundance	100 mM
5	calcium chloride	natural abundance	5 mM
6	sodium chloride	natural abundance	100 mM

15 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details SyR11.004

#	Name	Isotope labeling	Concentration
13	SyR11	[U-5% 13C; U-100% 15N]	0.94 mM
14	MES	natural abundance	20 mM
15	sodium azide	natural abundance	0.02 %
16	DTT	natural abundance	100 mM
17	calcium chloride	natural abundance	5 mM
18	sodium chloride	natural abundance	100 mM

16 2D 1H-13C HSQC (arom)

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details SyR11.009

#	Name	Isotope labeling	Concentration
1	SyR11	[U-100% 13C; U-100% 15N]	0.66 mM
2	MES	natural abundance	20 mM
3	sodium azide	natural abundance	0.02 %
4	DTT	natural abundance	100 mM
5	calcium chloride	natural abundance	5 mM
6	sodium chloride	natural abundance	100 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr15335_3.str
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

Content subtype: bmr15335_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1740		96.3 (chain: 1, length: 163)
1	Chemical shift references	chemical_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 163, Sequence coverage: 96.3%
- Total number of assignments
  - ¹H chemical shifts: 954
  - ¹³C chemical shifts: 608
  - ¹⁵N chemical shifts: 178
- Completeness of assignments
  - Entity_assemble_ID: 1
- 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: 1

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
109	HIS	ND1	246.1
109	HIS	NE2	170.6
153	HIS	ND1	196.9
153	HIS	NE2	177.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	851	792	93.1
¹³C chemical shifts	656	608	92.7
¹⁵N chemical shifts	185	174	94.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	342	324	94.7
¹³C chemical shifts	326	312	95.7
¹⁵N chemical shifts	160	150	93.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	509	468	91.9
¹³C chemical shifts	330	296	89.7
¹⁵N chemical shifts	25	24	96.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	84	81	96.4
¹³C chemical shifts	84	81	96.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	77	61	79.2
¹³C chemical shifts	74	54	73.0
¹⁵N chemical shifts	3	3	100.0

Keywords Amidase, CHAP domain, NESG, NMR

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 (0.788 seconds)

BMRB: 15335

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. SyR11, : 1 : 1 entities Detail

Experiments performed 16 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

Chemical shift validation 3 contents Detail