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BMRB: 25770

5LGF

N-terminal domain of the telomerase catalytic subunit Est2 from Ogataea polymorpha

Authors

Polshakov, V., Efimov, S., Petrova, O., Zvereva, M.

Assembly

N Est2

Entity

1. N Est2 (polymer, Thiol state: all free), 159 monomers, 18563.60 Da Detail

MRFDQYVDEN KSSDDFEPLI HDLFETRWHG TGREIWIERV KDRKIPSTLV KPNYSHEELI DMLIGYLADN RYENALINGL VTGDDLEIAN SYGFKGRNAV TNLLKSPEFR LVHTIIGTET FLDLLINYSA RMGNVYLWGE LNESNYKTQC KSSENLYFQ

Formula weight

18563.6 Da

Source organism

Ogataea polymorpha

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 89.9 %, Completeness: 73.8 %, Completeness (bb): 85.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	73.8 % (1410 of 1910)	73.3 % (727 of 992)	72.8 % (542 of 744)	81.0 % (141 of 174)
Backbone	85.5 % (809 of 946)	84.9 % (275 of 324)	86.7 % (405 of 467)	83.2 % (129 of 155)
Sidechain	65.9 % (733 of 1113)	67.7 % (452 of 668)	62.9 % (268 of 426)	68.4 % (13 of 19)
Aromatic	30.4 % (59 of 194)	40.2 % (39 of 97)	18.1 % (17 of 94)	100.0 % (3 of 3)
Methyl	89.5 % (154 of 172)	91.9 % (79 of 86)	87.2 % (75 of 86)

1. TEN

MRFDQYVDEN KSSDDFEPLI HDLFETRWHG TGREIWIERV KDRKIPSTLV KPNYSHEELI DMLIGYLADN RYENALINGL VTGDDLEIAN SYGFKGRNAV TNLLKSPEFR LVHTIIGTET FLDLLINYSA RMGNVYLWGE LNESNYKTQC KSSENLYFQ

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	TEN	[U-99% 13C; U-99% 15N]	protein	0.5 mM
2	sodium phosphate	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	50 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.02 % w/v
6	H2O	natural abundance	solvent	90 %
7	D2O	[U-2H]	solvent	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
8	TEN	[U-99% 15N]	protein	0.8 mM
9	sodium phosphate	natural abundance	buffer	20 mM
10	sodium chloride	natural abundance	salt	50 mM
11	DTT	natural abundance		1 mM
12	sodium azide	natural abundance		0.02 % w/v
13	H2O	natural abundance	solvent	90 %
14	D2O	[U-2H]	solvent	10 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
15	TEN	[U-99% 13C; U-99% 15N]	protein	0.5 mM
16	sodium phosphate	natural abundance	buffer	20 mM
17	sodium chloride	natural abundance	salt	50 mM
18	DTT	natural abundance		1 mM
19	sodium azide	natural abundance		0.02 % w/v
20	D2O	[U-2H]	solvent	100 %

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
21	TEN	natural abundance	protein	1.0 mM
22	sodium phosphate	natural abundance	buffer	20 mM
23	sodium chloride	natural abundance	salt	50 mM
24	DTT	natural abundance		1 mM
25	sodium azide	natural abundance		0.02 % w/v
26	H2O	natural abundance	solvent	90 %
27	D2O	[U-2H]	solvent	10 %

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: -0.18 ppm, Outliers: 1 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: -0.18 ppm, Outliers: 1 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: 0.02 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: 0.14 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 5LGF, Strand ID: A Detail

Release date

2016-10-27

Citation

NMR assignments of the N-terminal domain of Ogataea polymorpha telomerase reverse transcriptase
Polshakov, V., Petrova, O., Parfenova, Y., Efimov, S., Klochkov, V., Zvereva, M., Dontsova, O.
Biomol. NMR Assign. (2015), 10, 183-187, PubMed 26721464 , DOI 10.1007/s12104-015-9663-6 , Abstract

Experiments performed 19 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	TEN	[U-99% 13C; U-99% 15N]	protein	0.5 mM
2	sodium phosphate	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	50 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.02 % w/v
6	H2O	natural abundance	solvent	90 %
7	D2O	[U-2H]	solvent	10 %

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
15	TEN	[U-99% 13C; U-99% 15N]	protein	0.5 mM
16	sodium phosphate	natural abundance	buffer	20 mM
17	sodium chloride	natural abundance	salt	50 mM
18	DTT	natural abundance		1 mM
19	sodium azide	natural abundance		0.02 % w/v
20	D2O	[U-2H]	solvent	100 %

3 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
15	TEN	[U-99% 13C; U-99% 15N]	protein	0.5 mM
16	sodium phosphate	natural abundance	buffer	20 mM
17	sodium chloride	natural abundance	salt	50 mM
18	DTT	natural abundance		1 mM
19	sodium azide	natural abundance		0.02 % w/v
20	D2O	[U-2H]	solvent	100 %

4 3D HNCO

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	TEN	[U-99% 13C; U-99% 15N]	protein	0.5 mM
2	sodium phosphate	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	50 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.02 % w/v
6	H2O	natural abundance	solvent	90 %
7	D2O	[U-2H]	solvent	10 %

5 3D HCACO

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	TEN	[U-99% 13C; U-99% 15N]	protein	0.5 mM
2	sodium phosphate	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	50 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.02 % w/v
6	H2O	natural abundance	solvent	90 %
7	D2O	[U-2H]	solvent	10 %

6 3D HNCA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	TEN	[U-99% 13C; U-99% 15N]	protein	0.5 mM
2	sodium phosphate	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	50 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.02 % w/v
6	H2O	natural abundance	solvent	90 %
7	D2O	[U-2H]	solvent	10 %

7 3D HN(CO)CA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	TEN	[U-99% 13C; U-99% 15N]	protein	0.5 mM
2	sodium phosphate	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	50 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.02 % w/v
6	H2O	natural abundance	solvent	90 %
7	D2O	[U-2H]	solvent	10 %

8 3D HNCACB

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	TEN	[U-99% 13C; U-99% 15N]	protein	0.5 mM
2	sodium phosphate	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	50 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.02 % w/v
6	H2O	natural abundance	solvent	90 %
7	D2O	[U-2H]	solvent	10 %

9 3D CBCA(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	TEN	[U-99% 13C; U-99% 15N]	protein	0.5 mM
2	sodium phosphate	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	50 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.02 % w/v
6	H2O	natural abundance	solvent	90 %
7	D2O	[U-2H]	solvent	10 %

10 3D HBHA(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	TEN	[U-99% 13C; U-99% 15N]	protein	0.5 mM
2	sodium phosphate	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	50 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.02 % w/v
6	H2O	natural abundance	solvent	90 %
7	D2O	[U-2H]	solvent	10 %

11 3D HBHANH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	TEN	[U-99% 13C; U-99% 15N]	protein	0.5 mM
2	sodium phosphate	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	50 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.02 % w/v
6	H2O	natural abundance	solvent	90 %
7	D2O	[U-2H]	solvent	10 %

12 3D HNHA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
8	TEN	[U-99% 15N]	protein	0.8 mM
9	sodium phosphate	natural abundance	buffer	20 mM
10	sodium chloride	natural abundance	salt	50 mM
11	DTT	natural abundance		1 mM
12	sodium azide	natural abundance		0.02 % w/v
13	H2O	natural abundance	solvent	90 %
14	D2O	[U-2H]	solvent	10 %

13 3D HNHB

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
8	TEN	[U-99% 15N]	protein	0.8 mM
9	sodium phosphate	natural abundance	buffer	20 mM
10	sodium chloride	natural abundance	salt	50 mM
11	DTT	natural abundance		1 mM
12	sodium azide	natural abundance		0.02 % w/v
13	H2O	natural abundance	solvent	90 %
14	D2O	[U-2H]	solvent	10 %

14 3D 1H-15N TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
8	TEN	[U-99% 15N]	protein	0.8 mM
9	sodium phosphate	natural abundance	buffer	20 mM
10	sodium chloride	natural abundance	salt	50 mM
11	DTT	natural abundance		1 mM
12	sodium azide	natural abundance		0.02 % w/v
13	H2O	natural abundance	solvent	90 %
14	D2O	[U-2H]	solvent	10 %

15 3D 1H-15N NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
8	TEN	[U-99% 15N]	protein	0.8 mM
9	sodium phosphate	natural abundance	buffer	20 mM
10	sodium chloride	natural abundance	salt	50 mM
11	DTT	natural abundance		1 mM
12	sodium azide	natural abundance		0.02 % w/v
13	H2O	natural abundance	solvent	90 %
14	D2O	[U-2H]	solvent	10 %

16 3D 1H-13C NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
15	TEN	[U-99% 13C; U-99% 15N]	protein	0.5 mM
16	sodium phosphate	natural abundance	buffer	20 mM
17	sodium chloride	natural abundance	salt	50 mM
18	DTT	natural abundance		1 mM
19	sodium azide	natural abundance		0.02 % w/v
20	D2O	[U-2H]	solvent	100 %

17 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
8	TEN	[U-99% 15N]	protein	0.8 mM
9	sodium phosphate	natural abundance	buffer	20 mM
10	sodium chloride	natural abundance	salt	50 mM
11	DTT	natural abundance		1 mM
12	sodium azide	natural abundance		0.02 % w/v
13	H2O	natural abundance	solvent	90 %
14	D2O	[U-2H]	solvent	10 %

18 3D HCCH-TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
15	TEN	[U-99% 13C; U-99% 15N]	protein	0.5 mM
16	sodium phosphate	natural abundance	buffer	20 mM
17	sodium chloride	natural abundance	salt	50 mM
18	DTT	natural abundance		1 mM
19	sodium azide	natural abundance		0.02 % w/v
20	D2O	[U-2H]	solvent	100 %

19 2D DQF-COSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
21	TEN	natural abundance	protein	1.0 mM
22	sodium phosphate	natural abundance	buffer	20 mM
23	sodium chloride	natural abundance	salt	50 mM
24	DTT	natural abundance		1 mM
25	sodium azide	natural abundance		0.02 % w/v
26	H2O	natural abundance	solvent	90 %
27	D2O	[U-2H]	solvent	10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25770_5lgf.nef
Input source #2: Coordindates	5lgf.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
MRFDQYVDENKSSDDFEPLIHDLFETRWHGTGREIWIERVKDRKIPSTLVKPNYSHEELIDMLIGYLADNRYENALINGLVTGDDLEIANSYGFKGRNAV
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MRFDQYVDENKSSDDFEPLIHDLFETRWHGTGREIWIERVKDRKIPSTLVKPNYSHEELIDMLIGYLADNRYENALINGLVTGDDLEIANSYGFKGRNAV

-------110-------120-------130-------140-------150---------
TNLLKSPEFRLVHTIIGTETFLDLLINYSARMGNVYLWGELNESNYKTQCKSSENLYFQ
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
TNLLKSPEFRLVHTIIGTETFLDLLINYSARMGNVYLWGELNESNYKTQCKSSENLYFQ

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	159	0	0	100.0

Content subtype: combined_25770_5lgf.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1335		89.3 (chain: A, length: 159)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1630 (1)	noe	91.2 (chain: A, length: 159)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	198 (198)	.	72.3 (chain: A, length: 159)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 159, Sequence coverage: 89.3%
- Total number of assignments
  - ¹H chemical shifts: 676
  - ¹³C chemical shifts: 521
  - ¹⁵N chemical shifts: 138
- 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)
5	GLN	CD	179.946
149	GLN	CD	180.346
159	GLN	CD	181.156

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	992	676	68.1
¹³C chemical shifts	744	518	69.6
¹⁵N chemical shifts	183	138	75.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	324	268	82.7
¹³C chemical shifts	318	272	85.5
¹⁵N chemical shifts	155	125	80.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	668	408	61.1
¹³C chemical shifts	426	246	57.7
¹⁵N chemical shifts	28	13	46.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	89	80	89.9
¹³C chemical shifts	89	74	83.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	97	35	36.1
¹³C chemical shifts	94	15	16.0
¹⁵N chemical shifts	3	3	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 159, Sequence coverage: 91.2%
- Total number of restraints: 1630
- Weight of restraints: 1.0 (1630)
- Potential type of restraints: square-well-parabolic (1630)
- Range of distance target values: 1.25, 4.45 (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: 159, Sequence coverage: 72.3%
- Total number of restraints: 198
- Total number of restraints per polymer type: 198
- Weight of restraints: 1.0 (198)
- Potential type of restraints: square-well-parabolic (198)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Protein structure and dynamics, Telomerase, Telomerase reverse transcriptase

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Found 1 Document (0.663 seconds)

BMRB: 25770

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Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Experiments performed 19 experiments Detail

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NMR combined restraints 4 contents Detail