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BMRB: 17745

2LSN

NMR Assignment of PFV RNase H domain

Authors

Leo, B., Schweimer, K., Woehrl, B.

Assembly

PFV RNase H

Entity

1. PFV RNase H (polymer, Thiol state: all free), 165 monomers, 18033.31 Da Detail

GAMGQYEGVF YTDGSAIKSP DPTKSNNAGM GIVHATYKPE YQVLNQWSIP LGNHTAQMAE IAAVEFACKK ALKIPGPVLV ITDSFYVAES ANKELPYWKS NGFVNNKKKP LKHISKWKSI AECLSMKPDI TIQHEKGHQP TNTSIHTEGN ALADKLATQG SYVVN

Formula weight

18033.31 Da

Source organism

Human spumaretrovirus

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.5 %, Completeness: 87.5 %, Completeness (bb): 92.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	87.5 % (1672 of 1911)	89.2 % (885 of 992)	85.5 % (635 of 743)	86.4 % (152 of 176)
Backbone	92.2 % (894 of 970)	92.2 % (306 of 332)	91.7 % (443 of 483)	93.5 % (145 of 155)
Sidechain	84.4 % (923 of 1094)	87.7 % (579 of 660)	81.6 % (337 of 413)	33.3 % (7 of 21)
Aromatic	62.8 % (98 of 156)	96.2 % (75 of 78)	26.7 % (20 of 75)	100.0 % (3 of 3)
Methyl	97.1 % (167 of 172)	96.5 % (83 of 86)	97.7 % (84 of 86)

1. PFV RNase H

GAMGQYEGVF YTDGSAIKSP DPTKSNNAGM GIVHATYKPE YQVLNQWSIP LGNHTAQMAE IAAVEFACKK ALKIPGPVLV ITDSFYVAES ANKELPYWKS NGFVNNKKKP LKHISKWKSI AECLSMKPDI TIQHEKGHQP TNTSIHTEGN ALADKLATQG SYVVN

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	PFV RNase H	[U-13C; U-15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: -0.17 ppm, Outliers: 3 Detail

LACS Plot; CB

Referencing offset: -0.17 ppm, Outliers: 3 Detail

LACS Plot; HA

Referencing offset: -0.01 ppm, Outliers: 4 Detail

LACS Plot; CO

Referencing offset: 0.02 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 19 models in PDB: 2LSN, Strand ID: A Detail

Release date

2012-03-26

Citation

Insights into the structure and activity of prototype foamy virus RNase H
Leo, B., Hartl, M.J., Schweimer, K., Mayr, F., Wohrl, B.M.
Retrovirology (2012), 9, 14-14, PubMed 22325739 , DOI 10.1186/1742-4690-9-14 , Abstract

Related entities 1. PFV RNase H, : 1 : 2 : 108 entities Detail

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz equipped with TCI-CryoProbe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	PFV RNase H	[U-13C; U-15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 700 MHz equipped with TCI-CryoProbe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	PFV RNase H	[U-13C; U-15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

3 3D HNCO

Instrument

Bruker Avance - 700 MHz equipped with TCI-CryoProbe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	PFV RNase H	[U-13C; U-15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

4 3D HNCA

Instrument

Bruker Avance - 700 MHz equipped with TCI-CryoProbe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	PFV RNase H	[U-13C; U-15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

5 3D HNCACB

Instrument

Bruker Avance - 700 MHz equipped with TCI-CryoProbe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	PFV RNase H	[U-13C; U-15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

6 3D CBCA(CO)NH

Instrument

Bruker Avance - 700 MHz equipped with TCI-CryoProbe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	PFV RNase H	[U-13C; U-15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

7 3D C(CO)NH

Instrument

Bruker Avance - 700 MHz equipped with TCI-CryoProbe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	PFV RNase H	[U-13C; U-15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

8 3D HBHA(CO)NH

Instrument

Bruker Avance - 700 MHz equipped with TCI-CryoProbe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	PFV RNase H	[U-13C; U-15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

9 3D HCCH-TOCSY

Instrument

Bruker Avance - 700 MHz equipped with TCI-CryoProbe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	PFV RNase H	[U-13C; U-15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

10 3D 1H-15N NOESY

Instrument

Bruker Avance - 700 MHz equipped with TCI-CryoProbe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	PFV RNase H	[U-13C; U-15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

11 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 700 MHz equipped with TCI-CryoProbe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	PFV RNase H	[U-13C; U-15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17745_2lsn.nef
Input source #2: Coordindates	2lsn.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
GAMGQYEGVFYTDGSAIKSPDPTKSNNAGMGIVHATYKPEYQVLNQWSIPLGNHTAQMAEIAAVEFACKKALKIPGPVLVITDSFYVAESANKELPYWKS
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GAMGQYEGVFYTDGSAIKSPDPTKSNNAGMGIVHATYKPEYQVLNQWSIPLGNHTAQMAEIAAVEFACKKALKIPGPVLVITDSFYVAESANKELPYWKS

-------110-------120-------130-------140-------150-------160-----
NGFVNNKKKPLKHISKWKSIAECLSMKPDITIQHEKGHQPTNTSIHTEGNALADKLATQGSYVVN
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NGFVNNKKKPLKHISKWKSIAECLSMKPDITIQHEKGHQPTNTSIHTEGNALADKLATQGSYVVN

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	165	0	0	100.0

Content subtype: combined_17745_2lsn.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1580		92.7 (chain: A, length: 165)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1841 (1)	noe	91.5 (chain: A, length: 165)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	148 (1)	noe	37.0 (chain: A, length: 165)
3	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	124 (1)	hbond	51.5 (chain: A, length: 165)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_5	OK	225 (225)	.	86.1 (chain: A, length: 165)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 165, Sequence coverage: 92.7%
- Total number of assignments
  - ¹³C chemical shifts: 600
  - ¹H chemical shifts: 838
  - ¹⁵N chemical shifts: 142
- Completeness of assignments
  - Entity_assemble_ID: A
- 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_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 165, Sequence coverage: 91.5%
- Total number of restraints: 1841
- Weight of restraints: 1.0 (1841)
- Potential type of restraints: square-well-parabolic (1841)
- Range of distance target values: 1.25, 3.0 (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_3
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 165, Sequence coverage: 37.0%
  - Total number of restraints: 148
  - Weight of restraints: 1.0 (148)
  - Potential type of restraints: square-well-parabolic (148)
  - Range of distance target values: 1.5, 3.0 (Å)
  - Histogram of 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: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 165, Sequence coverage: 51.5%
    - Total number of restraints: 124
    - Weight of restraints: 1.0 (124)
    - Potential type of restraints: square-well-parabolic (124)
    - Range of distance target values: 1.15, 1.65 (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_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 165, Sequence coverage: 86.1%
- Total number of restraints: 225
- Total number of restraints per polymer type: 225
- Weight of restraints: 1.0 (225)
- Potential type of restraints: square-well-parabolic (225)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A