BMRBj - BMREntryMaster

	Total	¹H	¹³C	¹⁵N
All	97.5 % (1353 of 1388)	98.2 % (721 of 734)	96.2 % (508 of 528)	98.4 % (124 of 126)
Backbone	99.0 % (671 of 678)	98.7 % (227 of 230)	99.1 % (338 of 341)	99.1 % (106 of 107)
Sidechain	96.6 % (791 of 819)	98.0 % (494 of 504)	94.3 % (279 of 296)	94.7 % (18 of 19)
Aromatic	77.8 % (56 of 72)	100.0 % (36 of 36)	55.6 % (20 of 36)
Methyl	100.0 % (130 of 130)	100.0 % (65 of 65)	100.0 % (65 of 65)

1. entity 1

GPLGSATLSD EAFIEQFRQE LLNNQMLRSQ LILQIPGLND LVNDPLLFRE RLGPLILQRR YGGYNTAMNP FGIPQDEYTR LMANPDDPDN KKRIAELLDQ QAIDEQLRNA IEYTPE

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5, Details 0.5 mM [U-13C; U-15N] Ddi1 86-196, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Ddi1 86-196-1	[U-13C; U-15N]		0.5 (±0.1) mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5, Details 0.5 mM [U-15N] Ddi1 86-196, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
2	Ddi1 86-196-2	[U-15N]		0.5 (±0.1) 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: -0.23 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: -0.23 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: -0.02 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: -0.15 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2016-09-29

Citation

Structural studies of the yeast DNA damage-inducible protein Ddi1 reveal domain architecture of this eukaryotic protein family
Trempe, J.F., Saskova, K.G., Siva, M., Ratcliffe, C.D., Veverka, V., Hoegl, A., Menade, M., Feng, X., Shenker, S., Svoboda, M., Kozisek, M., Konvalinka, J., Gehring, K.
Sci. Rep. (2016), 6, 33671-33671, PubMed 27646017 , DOI 10.1038/srep33671 , Abstract

Related entities 1. DNA damage-inducible protein 1, : 20 entities Detail

Interaction partners 1. DNA damage-inducible protein 1, : 10 interactors Detail

More details for 10 interactors identified by 7 citations

Experiments performed 9 experiments Detail

1 2D 1H-15N het NOE

Instrument

Bruker Avance - 600 MHz RT probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5, Details 0.5 mM [U-15N] Ddi1 86-196, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
2	Ddi1 86-196-2	[U-15N]		0.5 (±0.1) mM

2 2D 1H-15N HSQC-IPAP

Instrument

Bruker Avance - 600 MHz RT probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5, Details 0.5 mM [U-15N] Ddi1 86-196, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
2	Ddi1 86-196-2	[U-15N]		0.5 (±0.1) mM

3 2D 1H-15N HSQC-IPAP

Instrument

Bruker Avance - 600 MHz RT probe

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5, Details 0.5 mM [U-15N] Ddi1 86-196, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
2	Ddi1 86-196-2	[U-15N]		0.5 (±0.1) mM

4 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz RT probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5, Details 0.5 mM [U-13C; U-15N] Ddi1 86-196, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Ddi1 86-196-1	[U-13C; U-15N]		0.5 (±0.1) mM

5 3D HNCACB

Instrument

Bruker Avance - 600 MHz RT probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5, Details 0.5 mM [U-13C; U-15N] Ddi1 86-196, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Ddi1 86-196-1	[U-13C; U-15N]		0.5 (±0.1) mM

6 3D 15N/1H NOESY-HSQC

Instrument

Bruker Avance - 850 MHz cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5, Details 0.5 mM [U-13C; U-15N] Ddi1 86-196, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Ddi1 86-196-1	[U-13C; U-15N]		0.5 (±0.1) mM

7 3D 13C/1H HSQC-NOESY

Instrument

Bruker Avance - 850 MHz cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5, Details 0.5 mM [U-13C; U-15N] Ddi1 86-196, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Ddi1 86-196-1	[U-13C; U-15N]		0.5 (±0.1) mM

8 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz RT probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5, Details 0.5 mM [U-15N] Ddi1 86-196, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
2	Ddi1 86-196-2	[U-15N]		0.5 (±0.1) mM

9 2D 1H-15N HSQC

Instrument

Bruker Avance - 850 MHz cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5, Details 0.5 mM [U-13C; U-15N] Ddi1 86-196, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Ddi1 86-196-1	[U-13C; U-15N]		0.5 (±0.1) mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_30102_5kes.nef
Input source #2: Coordindates	5kes.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

--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180
GPLGSATLSDEAFIEQFRQELLNNQMLRSQLILQIPGLNDLVNDPLLFRERLGPLILQRRYGGYNTAMNPFGIPQDEYTRLMANPDDPDNKKRIAELLDQ
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GPLGSATLSDEAFIEQFRQELLNNQMLRSQLILQIPGLNDLVNDPLLFRERLGPLILQRRYGGYNTAMNPFGIPQDEYTRLMANPDDPDNKKRIAELLDQ
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-------190------
QAIDEQLRNAIEYTPE
||||||||||||||||
QAIDEQLRNAIEYTPE
-------110------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	116	0	0	100.0

Content subtype: combined_30102_5kes.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1354		99.1 (chain: A, length: 116)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	2751 (1)	noe	82.8 (chain: A, length: 116)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	168 (168)	.	81.0 (chain: A, length: 116)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_4	OK	78 (78)	.	67.2 (chain: A, length: 116)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 116, Sequence coverage: 99.1%
- Total number of assignments
  - ¹H chemical shifts: 721
  - ¹³C chemical shifts: 507
  - ¹⁵N chemical shifts: 126
- Completeness of assignments
  - Entity_assemble_ID: A
- 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	734	721	98.2
¹³C chemical shifts	528	507	96.0
¹⁵N chemical shifts	135	126	93.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	230	227	98.7
¹³C chemical shifts	232	229	98.7
¹⁵N chemical shifts	107	106	99.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	504	494	98.0
¹³C chemical shifts	296	278	93.9
¹⁵N chemical shifts	28	20	71.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	68	68	100.0
¹³C chemical shifts	68	68	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	36	36	100.0
¹³C chemical shifts	36	19	52.8

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 116, Sequence coverage: 82.8%
- Total number of restraints: 2751
- Weight of restraints: 1.0 (2751)
- Potential type of restraints: square-well-parabolic (2751)
- Range of distance target values: 1.26, 3.05 (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: 116, Sequence coverage: 81.0%
- Total number of restraints: 168
- Total number of restraints per polymer type: 168
- Weight of restraints: 1.0 (168)
- Potential type of restraints: square-well-parabolic (168)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_4

Status: OK
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 116, Sequence coverage: 67.2%

--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180
GPLGSATLSDEAFIEQFRQELLNNQMLRSQLILQIPGLNDLVNDPLLFRERLGPLILQRRYGGYNTAMNPFGIPQDEYTRLMANPDDPDNKKRIAELLDQ
         |||| ||||||||||| ||||||||| |||||||| | |||||| |||||||         ||| |||||| ||| || ||||||||||||
.........DEAF.EQFRQELLNNQ.LRSQLILQI.GLNDLVND.L.FRERLG.LILQRRY.........FGI.QDEYTR.MAN.DD.DNKKRIAELLDQ
--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180

-------190------
QAIDEQLRNAIEYTPE
| |||||         
Q.IDEQL         
-------

Total number of restraints: 78
Potential type of restraints: undefined (78)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None

Keywords DNA repair, UNKNOWN FUNCTION, helical bundles

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Found 1 Document (0.859 seconds)

BMRB: 30102

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. DNA damage-inducible protein 1, : 20 entities Detail

Interaction partners 1. DNA damage-inducible protein 1, : 10 interactors Detail

Experiments performed 9 experiments Detail

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NMR combined restraints 5 contents Detail