BMRBj - BMREntryMaster

Found 1 Document (0.712 seconds)

BMRB: 15916

2K7I

Solution NMR structure of protein ATU0232 from AGROBACTERIUM TUMEFACIENS. Northeast Structural Genomics Consortium (NESG) target AtT3. Ontario Center for Structural Proteomics target ATC0223.

Authors

Lemak, A., Srisailam, S., Yee, A., Bansal, S., Semesi, A., Prestegard, J., Arrowsmith, C.

Assembly

ATU0232

Entity

1. ATU0232 (polymer, Thiol state: not present), 83 monomers, 9360.226 × 2 Da Detail

MGSSHHHHHH SSGRENLYFQ GMYKFEIYQD KAGEYRFRFK ASNGETMFSS EGYKAKASAI HAIESIKRNS AGADTVDLTT MTA

Total weight

18720.451 Da

Max. entity weight

9360.226 Da

Source organism

Agrobacterium tumefaciens

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 78.3 %, Completeness: 66.6 %, Completeness (bb): 73.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	66.6 % (629 of 944)	66.6 % (325 of 488)	66.0 % (243 of 368)	69.3 % (61 of 88)
Backbone	73.1 % (364 of 498)	72.8 % (126 of 173)	74.0 % (179 of 242)	71.1 % (59 of 83)
Sidechain	61.3 % (320 of 522)	63.2 % (199 of 315)	58.9 % (119 of 202)	40.0 % (2 of 5)
Aromatic	35.6 % (42 of 118)	45.8 % (27 of 59)	25.4 % (15 of 59)
Methyl	87.5 % (49 of 56)	85.7 % (24 of 28)	89.3 % (25 of 28)

1. Atc0223

MGSSHHHHHH SSGRENLYFQ GMYKFEIYQD KAGEYRFRFK ASNGETMFSS EGYKAKASAI HAIESIKRNS AGADTVDLTT MTA

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.7

#	Name	Isotope labeling	Concentration
1	Atc0223	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride	natural abundance	500 mM
4	ZnSO4	natural abundance	10 uM
5	DTT	natural abundance	10 mM
6	NaN3	natural abundance	0.01 %
7	Benzamidine	natural abundance	10 mM
8	H2O	natural abundance	90 %
9	D20	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.7

#	Name	Isotope labeling	Concentration
10	Atc0223	[U-13C; U-15N]	0.5 mM
11	TRIS	natural abundance	10 mM
12	sodium chloride	natural abundance	500 mM
13	ZnSO4	natural abundance	10 uM
14	DTT	natural abundance	10 mM
15	NaN3	natural abundance	0.01 %
16	Benzamidine	natural abundance	10 mM
17	D20	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: -0.17 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: -0.17 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: -0.03 ppm, Outliers: 3 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: 0.1 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2K7I, Strand ID: A, B Detail

Release date

2010-09-23

Citation

Solution structure of protein ATC0223 from Agrobacterium Tumefaciens
Lemak, A., Srisailam, S., Yee, A., Bansal, S., Semesi, A., Prestegard, J., Arrowsmith, C.
Not known

Related entities 1. ATU0232, : 1 : 4 entities Detail

Experiments performed 13 experiments Detail

1 3D HNCO

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.7

#	Name	Isotope labeling	Concentration
1	Atc0223	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride	natural abundance	500 mM
4	ZnSO4	natural abundance	10 uM
5	DTT	natural abundance	10 mM
6	NaN3	natural abundance	0.01 %
7	Benzamidine	natural abundance	10 mM
8	H2O	natural abundance	90 %
9	D20	natural abundance	10 %

2 3D HNCA

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.7

#	Name	Isotope labeling	Concentration
1	Atc0223	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride	natural abundance	500 mM
4	ZnSO4	natural abundance	10 uM
5	DTT	natural abundance	10 mM
6	NaN3	natural abundance	0.01 %
7	Benzamidine	natural abundance	10 mM
8	H2O	natural abundance	90 %
9	D20	natural abundance	10 %

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.7

#	Name	Isotope labeling	Concentration
1	Atc0223	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride	natural abundance	500 mM
4	ZnSO4	natural abundance	10 uM
5	DTT	natural abundance	10 mM
6	NaN3	natural abundance	0.01 %
7	Benzamidine	natural abundance	10 mM
8	H2O	natural abundance	90 %
9	D20	natural abundance	10 %

4 3D HBHA(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.7

#	Name	Isotope labeling	Concentration
1	Atc0223	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride	natural abundance	500 mM
4	ZnSO4	natural abundance	10 uM
5	DTT	natural abundance	10 mM
6	NaN3	natural abundance	0.01 %
7	Benzamidine	natural abundance	10 mM
8	H2O	natural abundance	90 %
9	D20	natural abundance	10 %

5 3D (H)C(CO)NH_TOCSY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.7

#	Name	Isotope labeling	Concentration
1	Atc0223	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride	natural abundance	500 mM
4	ZnSO4	natural abundance	10 uM
5	DTT	natural abundance	10 mM
6	NaN3	natural abundance	0.01 %
7	Benzamidine	natural abundance	10 mM
8	H2O	natural abundance	90 %
9	D20	natural abundance	10 %

6 3D H(CCO)NH_TOCSY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.7

#	Name	Isotope labeling	Concentration
1	Atc0223	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride	natural abundance	500 mM
4	ZnSO4	natural abundance	10 uM
5	DTT	natural abundance	10 mM
6	NaN3	natural abundance	0.01 %
7	Benzamidine	natural abundance	10 mM
8	H2O	natural abundance	90 %
9	D20	natural abundance	10 %

7 3D H(C)CH-TOCSY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.7

#	Name	Isotope labeling	Concentration
10	Atc0223	[U-13C; U-15N]	0.5 mM
11	TRIS	natural abundance	10 mM
12	sodium chloride	natural abundance	500 mM
13	ZnSO4	natural abundance	10 uM
14	DTT	natural abundance	10 mM
15	NaN3	natural abundance	0.01 %
16	Benzamidine	natural abundance	10 mM
17	D20	natural abundance	100 %

8 3D (H)CCH-TOCSY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.7

#	Name	Isotope labeling	Concentration
10	Atc0223	[U-13C; U-15N]	0.5 mM
11	TRIS	natural abundance	10 mM
12	sodium chloride	natural abundance	500 mM
13	ZnSO4	natural abundance	10 uM
14	DTT	natural abundance	10 mM
15	NaN3	natural abundance	0.01 %
16	Benzamidine	natural abundance	10 mM
17	D20	natural abundance	100 %

9 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.7

#	Name	Isotope labeling	Concentration
1	Atc0223	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride	natural abundance	500 mM
4	ZnSO4	natural abundance	10 uM
5	DTT	natural abundance	10 mM
6	NaN3	natural abundance	0.01 %
7	Benzamidine	natural abundance	10 mM
8	H2O	natural abundance	90 %
9	D20	natural abundance	10 %

10 3D 1H-13C NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.7

#	Name	Isotope labeling	Concentration
1	Atc0223	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride	natural abundance	500 mM
4	ZnSO4	natural abundance	10 uM
5	DTT	natural abundance	10 mM
6	NaN3	natural abundance	0.01 %
7	Benzamidine	natural abundance	10 mM
8	H2O	natural abundance	90 %
9	D20	natural abundance	10 %

11 3D 1H-13C NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.7

#	Name	Isotope labeling	Concentration
10	Atc0223	[U-13C; U-15N]	0.5 mM
11	TRIS	natural abundance	10 mM
12	sodium chloride	natural abundance	500 mM
13	ZnSO4	natural abundance	10 uM
14	DTT	natural abundance	10 mM
15	NaN3	natural abundance	0.01 %
16	Benzamidine	natural abundance	10 mM
17	D20	natural abundance	100 %

12 3D 1H-13C_arom NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.7

#	Name	Isotope labeling	Concentration
1	Atc0223	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride	natural abundance	500 mM
4	ZnSO4	natural abundance	10 uM
5	DTT	natural abundance	10 mM
6	NaN3	natural abundance	0.01 %
7	Benzamidine	natural abundance	10 mM
8	H2O	natural abundance	90 %
9	D20	natural abundance	10 %

13 2D 1H-15N HSQC(IPAP)

Instrument

Varian INOVA - 600 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.7

#	Name	Isotope labeling	Concentration
1	Atc0223	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride	natural abundance	500 mM
4	ZnSO4	natural abundance	10 uM
5	DTT	natural abundance	10 mM
6	NaN3	natural abundance	0.01 %
7	Benzamidine	natural abundance	10 mM
8	H2O	natural abundance	90 %
9	D20	natural abundance	10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_15916_2k7i.nef
Input source #2: Coordindates	2k7i.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--
MGSSHHHHHHSSGRENLYFQGMYKFEIYQDKAGEYRFRFKASNGETMFSSEGYKAKASAIHAIESIKRNSAGADTVDLTTMTA
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGSSHHHHHHSSGRENLYFQGMYKFEIYQDKAGEYRFRFKASNGETMFSSEGYKAKASAIHAIESIKRNSAGADTVDLTTMTA
--------10--------20--------30--------40--------50--------60--------70--------80---

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

-----------------------------10--------20--------30--------40--------50--------60--
MGSSHHHHHHSSGRENLYFQGMYKFEIYQDKAGEYRFRFKASNGETMFSSEGYKAKASAIHAIESIKRNSAGADTVDLTTMTA
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGSSHHHHHHSSGRENLYFQGMYKFEIYQDKAGEYRFRFKASNGETMFSSEGYKAKASAIHAIESIKRNSAGADTVDLTTMTA
--------10--------20--------30--------40--------50--------60--------70--------80---

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	83	0	0	100.0
B	B	83	0	0	100.0

Content subtype: combined_15916_2k7i.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	610		73.5 (chain: A, length: 83)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	3252 (1)	noe	73.5 (chain: A, length: 83), 73.5 (chain: B, length: 83)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	164 (164)	.	65.1 (chain: A, length: 83), 65.1 (chain: B, length: 83)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_4	OK	92 (92)	.	55.4 (chain: A, length: 83), 55.4 (chain: B, length: 83)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 83, Sequence coverage: 73.5%
- Total number of assignments
  - ¹H chemical shifts: 316
  - ¹³C chemical shifts: 235
  - ¹⁵N chemical shifts: 59
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	488	316	64.8
¹³C chemical shifts	368	235	63.9
¹⁵N chemical shifts	92	59	64.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	173	121	69.9
¹³C chemical shifts	166	120	72.3
¹⁵N chemical shifts	83	56	67.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	315	195	61.9
¹³C chemical shifts	202	115	56.9
¹⁵N chemical shifts	9	3	33.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	32	27	84.4
¹³C chemical shifts	32	27	84.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	59	27	45.8
¹³C chemical shifts	59	15	25.4

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 83, Sequence coverage: 73.5%
  - Entity_assembly_ID: B, Chain length: 83, Sequence coverage: 73.5%
- Total number of restraints: 3251
- Weight of restraints: 1.0 (3251)
- Potential type of restraints: square-well-parabolic (3251)
- 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
  - Chain_ID: B
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 83, Sequence coverage: 65.1%
  - Entity_assembly_ID: B, Chain length: 83, Sequence coverage: 65.1%
- Total number of restraints: 164
- Total number of restraints per polymer type: 164
- Weight of restraints: 1.0 (164)
- Potential type of restraints: square-well-parabolic (164)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_4

Status: OK
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 83, Sequence coverage: 55.4%

-----------------------------10--------20--------30--------40--------50--------60--
MGSSHHHHHHSSGRENLYFQGMYKFEIYQDKAGEYRFRFKASNGETMFSSEGYKAKASAIHAIESIKRNSAGADTVDLTTMTA
                       ||||||| ||||| ||||| || | || ||  ||||| || ||||||||| ||||||   
.......................KFEIYQD.AGEYR.RFKAS.GE.M.SS.GY..KASAI.AI.SIKRNSAGA.TVDLTT   
-----------------------------10--------20--------30--------40--------50---------

Entity_assembly_ID: B, Chain length: 83, Sequence coverage: 55.4%

-----------------------------10--------20--------30--------40--------50--------60--
MGSSHHHHHHSSGRENLYFQGMYKFEIYQDKAGEYRFRFKASNGETMFSSEGYKAKASAIHAIESIKRNSAGADTVDLTTMTA
                       ||||||| ||||| ||||| || | || ||  ||||| || ||||||||| ||||||   
.......................KFEIYQD.AGEYR.RFKAS.GE.M.SS.GY..KASAI.AI.SIKRNSAGA.TVDLTT   
-----------------------------10--------20--------30--------40--------50---------

Total number of restraints: 92
Potential type of restraints: undefined (92)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None
- Chain_ID: B
  None

Keywords protein of unknown function, swapped dimer

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 (0.712 seconds)

BMRB: 15916

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. ATU0232, : 1 : 4 entities Detail

Experiments performed 13 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

NMR combined restraints 5 contents Detail