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BMRB: 16810

2KW7

Solution NMR Structure of the N-terminal domain of protein PG_0361 from P.gingivalis, Northeast Structural Genomics Consortium Target Target PgR37A

Authors

Eletsky, A., Mills, J.L., Lee, D., Ciccosanti, C., Hamilton, K.B., Acton, T.B., Xiao, R.B., Everett, J.K., Montelione, G.T., Szyperski, T.

Assembly

PgR37A

Entity

1. PgR37A (polymer, Thiol state: not present), 157 monomers, 17522.57 Da Detail

MRVYKPEDVP NVQLADSTRL VTDEAGLLSN AQEEVMNGRL RAIRSSHAVE FAVVTLPSIG DAPLEDFTLK LARQWGVGNE KNNNGLLLVL VLDQRRVRFE TGYGLEGYLP DGLLSRIIHD RMIPHFRSGN YAEGLSEGVL AVQQVLDGSL EHHHHHH

Formula weight

17522.57 Da

Source organism

Porphyromonas gingivalis

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 97.5 %, Completeness: 95.3 %, Completeness (bb): 95.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	95.3 % (1711 of 1796)	95.2 % (884 of 929)	95.6 % (670 of 701)	94.6 % (157 of 166)
Backbone	95.5 % (888 of 930)	95.7 % (308 of 322)	95.8 % (438 of 457)	94.0 % (142 of 151)
Sidechain	95.3 % (962 of 1009)	94.9 % (576 of 607)	95.9 % (371 of 387)	100.0 % (15 of 15)
Aromatic	80.8 % (97 of 120)	81.7 % (49 of 60)	79.7 % (47 of 59)	100.0 % (1 of 1)
Methyl	99.0 % (196 of 198)	98.0 % (97 of 99)	100.0 % (99 of 99)

1. PgR37A

MRVYKPEDVP NVQLADSTRL VTDEAGLLSN AQEEVMNGRL RAIRSSHAVE FAVVTLPSIG DAPLEDFTLK LARQWGVGNE KNNNGLLLVL VLDQRRVRFE TGYGLEGYLP DGLLSRIIHD RMIPHFRSGN YAEGLSEGVL AVQQVLDGSL EHHHHHH

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.8 mM [U-100% 13C; U-100% 15N] PgR37A, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	PgR37A	[U-100% 13C; U-100% 15N]	0.8 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	calcium chloride	natural abundance	5 mM
5	sodium azide	natural abundance	0.02 %
6	DSS	natural abundance	50 uM
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.8 mM [U-5% 13C; U-100% 15N] PgR37A, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
9	PgR37A	[U-5% 13C; U-100% 15N]	0.8 mM
10	MES	natural abundance	20 mM
11	sodium chloride	natural abundance	100 mM
12	calcium chloride	natural abundance	5 mM
13	sodium azide	natural abundance	0.02 %
14	DSS	natural abundance	50 uM
15	H2O	natural abundance	95 %
16	D2O	natural abundance	5 %

LACS Plot; CA

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

Referencing offset: 0.21 ppm, Outliers: 3 Detail

LACS Plot; CB

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

Referencing offset: 0.21 ppm, Outliers: 3 Detail

LACS Plot; HA

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

Referencing offset: -0.05 ppm, Outliers: 2 Detail

LACS Plot; CO

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

Referencing offset: -0.03 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2KW7, Strand ID: A Detail

Release date

2010-04-27

Related entities 1. PgR37A, : 1 : 6 entities Detail

Experiments performed 14 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.8 mM [U-100% 13C; U-100% 15N] PgR37A, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	PgR37A	[U-100% 13C; U-100% 15N]	0.8 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	calcium chloride	natural abundance	5 mM
5	sodium azide	natural abundance	0.02 %
6	DSS	natural abundance	50 uM
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.8 mM [U-100% 13C; U-100% 15N] PgR37A, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	PgR37A	[U-100% 13C; U-100% 15N]	0.8 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	calcium chloride	natural abundance	5 mM
5	sodium azide	natural abundance	0.02 %
6	DSS	natural abundance	50 uM
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

3 3D HNCO

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.8 mM [U-100% 13C; U-100% 15N] PgR37A, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	PgR37A	[U-100% 13C; U-100% 15N]	0.8 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	calcium chloride	natural abundance	5 mM
5	sodium azide	natural abundance	0.02 %
6	DSS	natural abundance	50 uM
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

4 3D CBCA(CO)NH

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.8 mM [U-100% 13C; U-100% 15N] PgR37A, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	PgR37A	[U-100% 13C; U-100% 15N]	0.8 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	calcium chloride	natural abundance	5 mM
5	sodium azide	natural abundance	0.02 %
6	DSS	natural abundance	50 uM
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

5 3D HNCACB

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.8 mM [U-100% 13C; U-100% 15N] PgR37A, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	PgR37A	[U-100% 13C; U-100% 15N]	0.8 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	calcium chloride	natural abundance	5 mM
5	sodium azide	natural abundance	0.02 %
6	DSS	natural abundance	50 uM
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

6 3D HBHA(CO)NH

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.8 mM [U-100% 13C; U-100% 15N] PgR37A, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	PgR37A	[U-100% 13C; U-100% 15N]	0.8 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	calcium chloride	natural abundance	5 mM
5	sodium azide	natural abundance	0.02 %
6	DSS	natural abundance	50 uM
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

7 3D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.8 mM [U-100% 13C; U-100% 15N] PgR37A, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	PgR37A	[U-100% 13C; U-100% 15N]	0.8 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	calcium chloride	natural abundance	5 mM
5	sodium azide	natural abundance	0.02 %
6	DSS	natural abundance	50 uM
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

8 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.8 mM [U-100% 13C; U-100% 15N] PgR37A, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	PgR37A	[U-100% 13C; U-100% 15N]	0.8 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	calcium chloride	natural abundance	5 mM
5	sodium azide	natural abundance	0.02 %
6	DSS	natural abundance	50 uM
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

9 3D HCCH-COSY aliphatic

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.8 mM [U-100% 13C; U-100% 15N] PgR37A, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	PgR37A	[U-100% 13C; U-100% 15N]	0.8 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	calcium chloride	natural abundance	5 mM
5	sodium azide	natural abundance	0.02 %
6	DSS	natural abundance	50 uM
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

10 3D HCCH-COSY aromatic

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.8 mM [U-100% 13C; U-100% 15N] PgR37A, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	PgR37A	[U-100% 13C; U-100% 15N]	0.8 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	calcium chloride	natural abundance	5 mM
5	sodium azide	natural abundance	0.02 %
6	DSS	natural abundance	50 uM
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

11 3D HCCH-TOCSY

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.8 mM [U-100% 13C; U-100% 15N] PgR37A, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	PgR37A	[U-100% 13C; U-100% 15N]	0.8 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	calcium chloride	natural abundance	5 mM
5	sodium azide	natural abundance	0.02 %
6	DSS	natural abundance	50 uM
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

12 2D 1H-13C HSQC

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.8 mM [U-5% 13C; U-100% 15N] PgR37A, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
9	PgR37A	[U-5% 13C; U-100% 15N]	0.8 mM
10	MES	natural abundance	20 mM
11	sodium chloride	natural abundance	100 mM
12	calcium chloride	natural abundance	5 mM
13	sodium azide	natural abundance	0.02 %
14	DSS	natural abundance	50 uM
15	H2O	natural abundance	95 %
16	D2O	natural abundance	5 %

13 2D long-range 1H-15N HSQC for histidine

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.8 mM [U-100% 13C; U-100% 15N] PgR37A, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	PgR37A	[U-100% 13C; U-100% 15N]	0.8 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	calcium chloride	natural abundance	5 mM
5	sodium azide	natural abundance	0.02 %
6	DSS	natural abundance	50 uM
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

14 3D HN(CA)CO

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.8 mM [U-100% 13C; U-100% 15N] PgR37A, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	PgR37A	[U-100% 13C; U-100% 15N]	0.8 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	calcium chloride	natural abundance	5 mM
5	sodium azide	natural abundance	0.02 %
6	DSS	natural abundance	50 uM
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_16810_2kw7.nef
Input source #2: Coordindates	2kw7.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
MRVYKPEDVPNVQLADSTRLVTDEAGLLSNAQEEVMNGRLRAIRSSHAVEFAVVTLPSIGDAPLEDFTLKLARQWGVGNEKNNNGLLLVLVLDQRRVRFE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MRVYKPEDVPNVQLADSTRLVTDEAGLLSNAQEEVMNGRLRAIRSSHAVEFAVVTLPSIGDAPLEDFTLKLARQWGVGNEKNNNGLLLVLVLDQRRVRFE

-------110-------120-------130-------140-------150-------
TGYGLEGYLPDGLLSRIIHDRMIPHFRSGNYAEGLSEGVLAVQQVLDGSLEHHHHHH
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||
TGYGLEGYLPDGLLSRIIHDRMIPHFRSGNYAEGLSEGVLAVQQVLDGSLEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	157	0	0	100.0

Content subtype: combined_16810_2kw7.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1733		96.8 (chain: A, length: 157)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	5161 (1)	noe	96.8 (chain: A, length: 157)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	5161 (1)	noe	96.8 (chain: A, length: 157)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	154 (154)	.	63.1 (chain: A, length: 157)
2	Dihedral angle restraints	CNS/XPLOR_dihedral_5	OK	154 (154)	.	63.1 (chain: A, length: 157)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 157, Sequence coverage: 96.8%
- Total number of assignments
  - ¹H chemical shifts: 897
  - ¹³C chemical shifts: 667
  - ¹⁵N chemical shifts: 169
- Completeness of assignments
  - Entity_assemble_ID: A
- 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)
22	THR	HG1	7.125
29	SER	HG	5.941
47	HIS	ND1	224.341
47	HIS	NE2	170.13
55	THR	HG1	6.714
68	THR	HG1	6.007
119	HIS	ND1	192.453
119	HIS	NE2	186.903
125	HIS	ND1	238.085
125	HIS	NE2	168.216

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	929	893	96.1
¹³C chemical shifts	701	667	95.1
¹⁵N chemical shifts	178	163	91.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	322	310	96.3
¹³C chemical shifts	314	297	94.6
¹⁵N chemical shifts	151	139	92.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	607	583	96.0
¹³C chemical shifts	387	370	95.6
¹⁵N chemical shifts	27	24	88.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	102	102	100.0
¹³C chemical shifts	102	102	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	60	48	80.0
¹³C chemical shifts	59	47	79.7
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 157, Sequence coverage: 96.8%
- Total number of restraints: 5147
- Weight of restraints: 1.0 (5147)
- Potential type of restraints: square-well-parabolic (5147)
- Range of distance target values: 1.49, 3.42 (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_4
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 157, Sequence coverage: 96.8%
  - Total number of restraints: 5147
  - Weight of restraints: 1.0 (5147)
  - Potential type of restraints: square-well-parabolic (5147)
  - Range of distance target values: 1.49, 3.42 (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_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 157, Sequence coverage: 63.1%
- Total number of restraints: 154
- Total number of restraints per polymer type: 154
- Weight of restraints: 1.0 (154)
- Potential type of restraints: square-well-parabolic (154)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
- Saveframe: CNS/XPLOR_dihedral_5
  - Status: OK
  - Experiment type: .
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 157, Sequence coverage: 63.1%
  - Total number of restraints: 154
  - Total number of restraints per polymer type: 154
  - Weight of restraints: 1.0 (154)
  - Potential type of restraints: square-well-parabolic (154)
  - Plot of Phi-Psi angle restraints
  - Dihedral angle restraints per residue
    - Chain_ID: A

Keywords NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG), PSI-2, Protein NMR, Protein Structure Initiative, Structural Genomics, Target PgR37A

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Found 1 Document (0.728 seconds)

BMRB: 16810

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. PgR37A, : 1 : 6 entities Detail

Experiments performed 14 experiments Detail

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NMR combined restraints 6 contents Detail