BMRBj - BMREntryMaster

Found 1 Document (1.511 seconds)

BMRB: 34184

6EQY

4th KOW domain of human hSpt5

Authors

Zuber, P.K., Schweimer, K., Roesch, P., Woehrl, B.M.

Assembly

Transcription elongation factor SPT5

Entity

1. Transcription elongation factor SPT5 (polymer), 129 monomers, 14390.34 Da Detail

AMGSETASGV DVGGQHEWGE LVQLDPQTVG VIVRLERETF QVLNMYGKVV TVRHQAVTRK KDNRFAVALD SEQNNIHVKD IVKVIDGPHS GREGEIRHLF RSFAFLHCKK LVENGGMFVC KTRHLVLAG

Formula weight

14390.34 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.4 %, Completeness: 89.4 %, Completeness (bb): 94.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.4 % (1334 of 1493)	88.2 % (682 of 773)	90.4 % (525 of 581)	91.4 % (127 of 139)
Backbone	94.3 % (726 of 770)	93.7 % (252 of 269)	94.1 % (352 of 374)	96.1 % (122 of 127)
Sidechain	85.8 % (720 of 839)	85.3 % (430 of 504)	88.2 % (285 of 323)	41.7 % (5 of 12)
Aromatic	73.1 % (79 of 108)	77.8 % (42 of 54)	67.9 % (36 of 53)	100.0 % (1 of 1)
Methyl	98.7 % (156 of 158)	98.7 % (78 of 79)	98.7 % (78 of 79)

1. entity 1

AMGSETASGV DVGGQHEWGE LVQLDPQTVG VIVRLERETF QVLNMYGKVV TVRHQAVTRK KDNRFAVALD SEQNNIHVKD IVKVIDGPHS GREGEIRHLF RSFAFLHCKK LVENGGMFVC KTRHLVLAG

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.4, Details 0.6 mM [U-99% 13C; U-99% 15N] KOW4, 20 mM sodium phosphate, 20 mM sodium chloride, 0.5 mM DTT, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	KOW4	[U-99% 13C; U-99% 15N]	0.6 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	20 mM
4	DTT	natural abundance	0.5 mM

LACS Plot; CA

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

Referencing offset: -0.07 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: -0.07 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: -0.06 ppm, Outliers: 2 Detail

LACS Plot; CO

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

Referencing offset: 0.51 ppm, Outliers: 1 Detail

Release date

2018-10-07

Citation

Structure and nucleic acid binding properties of KOW domains 4 and 6-7 of human transcription elongation factor DSIF
Zuber, P.K., Hahn, L., Reinl, A., Schweimer, K., Knauer, S.H., Gottesman, M.E., Rosch, P., Wohrl, B.M.
Sci. Rep. (2018), 8, 11660-11660, PubMed 30076330 , DOI 10.1038/s41598-018-30042-3 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 34185 released on 2018-10-22
Title 6th KOW domain of human hSpt5

Related entities 1. Transcription elongation factor SPT5, : 1 : 8 : 38 entities Detail

Interaction partners 1. Transcription elongation factor SPT5, : 55 interactors Detail

More details for 55 interactors identified by 20 citations

Experiments performed 14 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 700 MHz cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.4, Details 0.6 mM [U-99% 13C; U-99% 15N] KOW4, 20 mM sodium phosphate, 20 mM sodium chloride, 0.5 mM DTT, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	KOW4	[U-99% 13C; U-99% 15N]	0.6 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	20 mM
4	DTT	natural abundance	0.5 mM

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker AvanceIII - 700 MHz cryoprobe

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.4, Details 0.6 mM [U-99% 13C; U-99% 15N] KOW4, 20 mM sodium phosphate, 20 mM sodium chloride, 0.5 mM DTT, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	KOW4	[U-99% 13C; U-99% 15N]	0.6 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	20 mM
4	DTT	natural abundance	0.5 mM

3 2D 1H-13C HSQC aromatic

Instrument

Bruker AvanceIII - 700 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	KOW4	[U-99% 13C; U-99% 15N]	0.6 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	20 mM
4	DTT	natural abundance	0.5 mM

4 3D HNCO

Instrument

Bruker AvanceIII - 700 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	KOW4	[U-99% 13C; U-99% 15N]	0.6 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	20 mM
4	DTT	natural abundance	0.5 mM

5 3D HNCA

Instrument

Bruker AvanceIII - 700 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	KOW4	[U-99% 13C; U-99% 15N]	0.6 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	20 mM
4	DTT	natural abundance	0.5 mM

6 3D 1H-13C NOESY aliphatic

Instrument

Bruker AvanceIII - 700 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	KOW4	[U-99% 13C; U-99% 15N]	0.6 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	20 mM
4	DTT	natural abundance	0.5 mM

7 3D 1H-15N NOESY

Instrument

Bruker AvanceIII - na MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	KOW4	[U-99% 13C; U-99% 15N]	0.6 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	20 mM
4	DTT	natural abundance	0.5 mM

8 3D CCH-TOCSY

Instrument

Bruker AvanceIII - 700 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	KOW4	[U-99% 13C; U-99% 15N]	0.6 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	20 mM
4	DTT	natural abundance	0.5 mM

9 3D HCCH-TOCSY

Instrument

Bruker AvanceIII - 700 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	KOW4	[U-99% 13C; U-99% 15N]	0.6 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	20 mM
4	DTT	natural abundance	0.5 mM

10 3D HBHA(CO)NH

Instrument

Bruker AvanceIII - 700 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	KOW4	[U-99% 13C; U-99% 15N]	0.6 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	20 mM
4	DTT	natural abundance	0.5 mM

11 3D HNCACB

Instrument

Bruker AvanceIII - 700 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	KOW4	[U-99% 13C; U-99% 15N]	0.6 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	20 mM
4	DTT	natural abundance	0.5 mM

12 3D C(CO)NH

Instrument

Bruker AvanceIII - 700 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	KOW4	[U-99% 13C; U-99% 15N]	0.6 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	20 mM
4	DTT	natural abundance	0.5 mM

13 3D CBCA(CO)NH

Instrument

Bruker AvanceIII - 700 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	KOW4	[U-99% 13C; U-99% 15N]	0.6 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	20 mM
4	DTT	natural abundance	0.5 mM

14 3D 1H-13C NOESY aromatic

Instrument

Bruker AvanceIII - 700 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	KOW4	[U-99% 13C; U-99% 15N]	0.6 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	20 mM
4	DTT	natural abundance	0.5 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_34184_6eqy.nef
Input source #2: Coordindates	6eqy.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-
AMGSETASGVDVGGQHEWGELVQLDPQTVGVIVRLERETFQVLNMYGKVVTVRHQAVTRKKDNRFAVALDSEQNNIHVKDIVKVIDGPHSGREGEIRHLF
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
AMGSETASGVDVGGQHEWGELVQLDPQTVGVIVRLERETFQVLNMYGKVVTVRHQAVTRKKDNRFAVALDSEQNNIHVKDIVKVIDGPHSGREGEIRHLF
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

------110-------120-------130
RSFAFLHCKKLVENGGMFVCKTRHLVLAG
|||||||||||||||||||||||||||||
RSFAFLHCKKLVENGGMFVCKTRHLVLAG
-------110-------120---------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	129	0	0	100.0

Content subtype: combined_34184_6eqy.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1330		98.4 (chain: A, length: 129)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	728 (1)	noe	86.0 (chain: A, length: 129)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	62 (1)	hbond	24.8 (chain: A, length: 129)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	120 (120)	.	77.5 (chain: A, length: 129)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 129, Sequence coverage: 98.4%
- Total number of assignments
  - ¹H chemical shifts: 682
  - ¹³C chemical shifts: 522
  - ¹⁵N chemical shifts: 126
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	773	682	88.2
¹³C chemical shifts	581	522	89.8
¹⁵N chemical shifts	148	126	85.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	269	255	94.8
¹³C chemical shifts	258	240	93.0
¹⁵N chemical shifts	127	121	95.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	504	427	84.7
¹³C chemical shifts	323	282	87.3
¹⁵N chemical shifts	21	5	23.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	82	81	98.8
¹³C chemical shifts	82	81	98.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	54	41	75.9
¹³C chemical shifts	53	34	64.2
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 129, Sequence coverage: 86.0%
- Total number of restraints: 726
- Weight of restraints: 1.0 (726)
- Potential type of restraints: square-well-parabolic (726)
- Range of distance target values: 1.5, 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_4
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 129, Sequence coverage: 24.8%
  - Total number of restraints: 62
  - Weight of restraints: 1.0 (62)
  - Potential type of restraints: square-well-parabolic (62)
  - 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_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 129, Sequence coverage: 77.5%
- Total number of restraints: 120
- Total number of restraints per polymer type: 120
- Weight of restraints: 1.0 (120)
- Potential type of restraints: square-well-parabolic (120)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords DSIF. transcription elongation, TRANSCRIPTION

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 (1.511 seconds)

BMRB: 34184

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. Transcription elongation factor SPT5, : 1 : 8 : 38 entities Detail

Interaction partners 1. Transcription elongation factor SPT5, : 55 interactors Detail

Experiments performed 14 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

Instrument

Sample

NMR combined restraints 5 contents Detail