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Found 1 Document (0.817 seconds)

BMRB: 19169

2M72

Solution structure of uncharacterized thioredoxin-like protein PG_2175 from Porphyromonas gingivalis

Authors

Harris, R., Ahmed, M., Attonito, J., Bonanno, J.B., Chamala, S., Chowdhury, S., Evans, B., Fiser, A., Glenn, A.S., Hammonds, J., Hillerich, B., Khafizov, K., Lafleur, J., Love, J.D., Seidel, R.D., Stead, M., Girvin, M.E., Almo, S.C.

Assembly

PG 2175

Entity

1. PG 2175 (polymer, Thiol state: not present), 156 monomers, 17355.51 Da Detail

MSLNTYAQLP AVSLKNIEGK TVQTNKLENA GKPMIISFFA TNCKPCLREL KAIQEVYADW QDETGVRLIA VSIDEGQNAQ KVKPLADGNG WEYEVLLDSN GDFKRAMNVS LIPAVFIVDG NGKIVYNHTG YTEGGEAELI KKVRELVKEG HHHHHH

Formula weight

17355.51 Da

Source organism

Porphyromonas gingivalis

Exptl. method

solution NMR

Refine. method

simulating annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.4 %, Completeness: 93.6 %, Completeness (bb): 96.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	93.6 % (1698 of 1814)	92.9 % (874 of 941)	94.2 % (662 of 703)	95.3 % (162 of 170)
Backbone	96.7 % (895 of 926)	96.2 % (308 of 320)	97.1 % (442 of 455)	96.0 % (145 of 151)
Sidechain	91.4 % (942 of 1031)	91.1 % (566 of 621)	91.8 % (359 of 391)	89.5 % (17 of 19)
Aromatic	80.3 % (106 of 132)	80.3 % (53 of 66)	79.7 % (51 of 64)	100.0 % (2 of 2)
Methyl	100.0 % (182 of 182)	100.0 % (91 of 91)	100.0 % (91 of 91)

1. PG 2175

MSLNTYAQLP AVSLKNIEGK TVQTNKLENA GKPMIISFFA TNCKPCLREL KAIQEVYADW QDETGVRLIA VSIDEGQNAQ KVKPLADGNG WEYEVLLDSN GDFKRAMNVS LIPAVFIVDG NGKIVYNHTG YTEGGEAELI KKVRELVKEG HHHHHH

Show sample condition

Sample #1

Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5, Details 10mM Na acetate buffer pH 4.5, 3mM DTT, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
1	PG_2175	[U-100% 13C; U-100% 15N]	1 mM
2	D20	natural abundance	10 %
3	H20	natural abundance	90 %
4	Na acetate buffer	natural abundance	10 mM
5	DTT	natural abundance	3 mM
6	EDTA	natural abundance	0.1 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5, Details 10mM Na acetate buffer pH 4.5, 3mM DTT, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
7	PG_2175	[U-100% 13C; U-100% 15N]	1 mM
8	D20	natural abundance	100 %
9	Na acetate buffer	natural abundance	10 mM
10	DTT	natural abundance	3 mM
11	EDTA	natural abundance	0.1 mM

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: 0.52 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: 0.52 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: -0.09 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	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: 3 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2M72, Strand ID: A Detail

Release date

2013-05-12

Related entities 1. PG 2175, : 1 : 44 entities Detail

Experiments performed 12 experiments Detail

1 15N HSQC

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5, Details 10mM Na acetate buffer pH 4.5, 3mM DTT, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
1	PG_2175	[U-100% 13C; U-100% 15N]	1 mM
2	D20	natural abundance	10 %
3	H20	natural abundance	90 %
4	Na acetate buffer	natural abundance	10 mM
5	DTT	natural abundance	3 mM
6	EDTA	natural abundance	0.1 mM

2 15N NOESY-HSQC

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5, Details 10mM Na acetate buffer pH 4.5, 3mM DTT, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
1	PG_2175	[U-100% 13C; U-100% 15N]	1 mM
2	D20	natural abundance	10 %
3	H20	natural abundance	90 %
4	Na acetate buffer	natural abundance	10 mM
5	DTT	natural abundance	3 mM
6	EDTA	natural abundance	0.1 mM

3 13C HSQC

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5, Details 10mM Na acetate buffer pH 4.5, 3mM DTT, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
7	PG_2175	[U-100% 13C; U-100% 15N]	1 mM
8	D20	natural abundance	100 %
9	Na acetate buffer	natural abundance	10 mM
10	DTT	natural abundance	3 mM
11	EDTA	natural abundance	0.1 mM

4 aromatic 13C HSQC

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5, Details 10mM Na acetate buffer pH 4.5, 3mM DTT, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
7	PG_2175	[U-100% 13C; U-100% 15N]	1 mM
8	D20	natural abundance	100 %
9	Na acetate buffer	natural abundance	10 mM
10	DTT	natural abundance	3 mM
11	EDTA	natural abundance	0.1 mM

5 13C NOESY-HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5, Details 10mM Na acetate buffer pH 4.5, 3mM DTT, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
7	PG_2175	[U-100% 13C; U-100% 15N]	1 mM
8	D20	natural abundance	100 %
9	Na acetate buffer	natural abundance	10 mM
10	DTT	natural abundance	3 mM
11	EDTA	natural abundance	0.1 mM

6 13C aromatic NOESY-HSQC

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5, Details 10mM Na acetate buffer pH 4.5, 3mM DTT, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
7	PG_2175	[U-100% 13C; U-100% 15N]	1 mM
8	D20	natural abundance	100 %
9	Na acetate buffer	natural abundance	10 mM
10	DTT	natural abundance	3 mM
11	EDTA	natural abundance	0.1 mM

7 HNCO

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5, Details 10mM Na acetate buffer pH 4.5, 3mM DTT, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
1	PG_2175	[U-100% 13C; U-100% 15N]	1 mM
2	D20	natural abundance	10 %
3	H20	natural abundance	90 %
4	Na acetate buffer	natural abundance	10 mM
5	DTT	natural abundance	3 mM
6	EDTA	natural abundance	0.1 mM

8 HNCACO

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5, Details 10mM Na acetate buffer pH 4.5, 3mM DTT, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
1	PG_2175	[U-100% 13C; U-100% 15N]	1 mM
2	D20	natural abundance	10 %
3	H20	natural abundance	90 %
4	Na acetate buffer	natural abundance	10 mM
5	DTT	natural abundance	3 mM
6	EDTA	natural abundance	0.1 mM

9 HNCA

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5, Details 10mM Na acetate buffer pH 4.5, 3mM DTT, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
1	PG_2175	[U-100% 13C; U-100% 15N]	1 mM
2	D20	natural abundance	10 %
3	H20	natural abundance	90 %
4	Na acetate buffer	natural abundance	10 mM
5	DTT	natural abundance	3 mM
6	EDTA	natural abundance	0.1 mM

10 HNCOCA

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5, Details 10mM Na acetate buffer pH 4.5, 3mM DTT, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
1	PG_2175	[U-100% 13C; U-100% 15N]	1 mM
2	D20	natural abundance	10 %
3	H20	natural abundance	90 %
4	Na acetate buffer	natural abundance	10 mM
5	DTT	natural abundance	3 mM
6	EDTA	natural abundance	0.1 mM

11 HNCACB

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5, Details 10mM Na acetate buffer pH 4.5, 3mM DTT, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
1	PG_2175	[U-100% 13C; U-100% 15N]	1 mM
2	D20	natural abundance	10 %
3	H20	natural abundance	90 %
4	Na acetate buffer	natural abundance	10 mM
5	DTT	natural abundance	3 mM
6	EDTA	natural abundance	0.1 mM

12 CBCACONH

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5, Details 10mM Na acetate buffer pH 4.5, 3mM DTT, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
1	PG_2175	[U-100% 13C; U-100% 15N]	1 mM
2	D20	natural abundance	10 %
3	H20	natural abundance	90 %
4	Na acetate buffer	natural abundance	10 mM
5	DTT	natural abundance	3 mM
6	EDTA	natural abundance	0.1 mM

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19169_2m72.nef
Input source #2: Coordindates	2m72.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
MSLNTYAQLPAVSLKNIEGKTVQTNKLENAGKPMIISFFATNCKPCLRELKAIQEVYADWQDETGVRLIAVSIDEGQNAQKVKPLADGNGWEYEVLLDSN
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MSLNTYAQLPAVSLKNIEGKTVQTNKLENAGKPMIISFFATNCKPCLRELKAIQEVYADWQDETGVRLIAVSIDEGQNAQKVKPLADGNGWEYEVLLDSN

-------110-------120-------130-------140-------150------
GDFKRAMNVSLIPAVFIVDGNGKIVYNHTGYTEGGEAELIKKVRELVKEGHHHHHH
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GDFKRAMNVSLIPAVFIVDGNGKIVYNHTGYTEGGEAELIKKVRELVKEGHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	156	0	0	100.0

Content subtype: combined_19169_2m72.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1692		96.2 (chain: A, length: 156)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	2477 (1)	noe	96.2 (chain: A, length: 156)
2	Distance restraints	CNS/XPLOR_distance_constraints_5	Warning	26 (1)	noe	18.6 (chain: A, length: 156)
3	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	90 (1)	hbond	41.0 (chain: A, length: 156)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	208 (208)	.	72.4 (chain: A, length: 156)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 156, Sequence coverage: 96.2%

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
MSLNTYAQLPAVSLKNIEGKTVQTNKLENAGKPMIISFFATNCKPCLRELKAIQEVYADWQDETGVRLIAVSIDEGQNAQKVKPLADGNGWEYEVLLDSN
   |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
...NTYAQLPAVSLKNIEGKTVQTNKLENAGKPMIISFFATNCKPCLRELKAIQEVYADWQDETGVRLIAVSIDEGQNAQKVKPLADGNGWEYEVLLDSN

-------110-------120-------130-------140-------150------
GDFKRAMNVSLIPAVFIVDGNGKIVYNHTGYTEGGEAELIKKVRELVKEGHHHHHH
|||||||||||||||||||||||||||||||||||||||||||||||||||   ||
GDFKRAMNVSLIPAVFIVDGNGKIVYNHTGYTEGGEAELIKKVRELVKEGH...HH

Total number of assignments
- ¹H chemical shifts: 860
- ¹³C chemical shifts: 669
- ¹⁵N chemical shifts: 163

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
4	ASN	CG	176.954
8	GLN	CD	180.573
16	ASN	CG	177.031
23	GLN	CD	180.248
24	THR	HG1	5.551
25	ASN	CG	177.78
42	ASN	CG	178.445
48	ARG	CZ	160.105
54	GLN	CD	179.333
61	GLN	CD	181.188
67	ARG	CZ	160.306
78	ASN	CG	176.312
89	ASN	CG	177.51
100	ASN	CG	177.759
105	ARG	CZ	159.589
108	ASN	CG	178.292
121	ASN	CG	177.777
127	ASN	CG	176.256
144	ARG	CZ	159.421

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	941	859	91.3
¹³C chemical shifts	703	651	92.6
¹⁵N chemical shifts	174	163	93.7

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	320	305	95.3
¹³C chemical shifts	312	300	96.2
¹⁵N chemical shifts	151	143	94.7

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	621	554	89.2
¹³C chemical shifts	391	351	89.8
¹⁵N chemical shifts	23	20	87.0

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	94	91	96.8
¹³C chemical shifts	94	91	96.8

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	66	51	77.3
¹³C chemical shifts	64	49	76.6
¹⁵N chemical shifts	2	2	100.0

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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 156, Sequence coverage: 96.2%
- Total number of restraints: 2473
- Weight of restraints: 1.0 (2473)
- Potential type of restraints: square-well-parabolic (2473)
- Range of distance target values: 2.4, 4.4 (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_5
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 156, Sequence coverage: 18.6%
  - Total number of restraints: 26
  - Weight of restraints: 1.0 (26)
  - Potential type of restraints: square-well-parabolic (26)
  - Range of distance target values: 2.65, 3.9 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_2
    - Status: OK
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 156, Sequence coverage: 41.0%
    - Total number of restraints: 90
    - Weight of restraints: 1.0 (90)
    - Potential type of restraints: square-well-parabolic (90)
    - Range of distance target values: 1.7, 2.7 (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_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 156, Sequence coverage: 72.4%
- Total number of restraints: 208
- Total number of restraints per polymer type: 208
- Weight of restraints: 1.0 (208)
- Potential type of restraints: square-well-parabolic (208)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords New York Structural Genomics Research Consortium, STRUCTURAL GENOMICS, THIOREDOXIN-LIKE, UNKNOWN FUNCTION

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Found 1 Document (0.817 seconds)

BMRB: 19169

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. PG 2175, : 1 : 44 entities Detail

Experiments performed 12 experiments Detail

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NMR combined restraints 6 contents Detail