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BMRB: 30097

5K57

HDD domain from human Ddi2

Authors

Assembly

Protein DDI1 homolog 2

Entity

1. Protein DDI1 homolog 2 (polymer, Thiol state: not present), 98 monomers, 11116.25 Da Detail

SQQSHSSPGE ITSSPQGLDN PALLRDMLLA NPHELSLLKE RNPPLAEALL SGDLEKFSRV LVEQQQDRAR REQERIRLFS ADPFDLEAQA KIEEDIRQ

Formula weight

11116.25 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.0 %, Completeness: 94.1 %, Completeness (bb): 98.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	94.1 % (1080 of 1148)	94.6 % (577 of 610)	93.3 % (406 of 435)	94.2 % (97 of 103)
Backbone	98.4 % (565 of 574)	97.9 % (188 of 192)	99.0 % (288 of 291)	97.8 % (89 of 91)
Sidechain	91.0 % (609 of 669)	93.1 % (389 of 418)	88.7 % (212 of 239)	66.7 % (8 of 12)
Aromatic	52.6 % (20 of 38)	78.9 % (15 of 19)	26.3 % (5 of 19)
Methyl	98.0 % (100 of 102)	100.0 % (51 of 51)	96.1 % (49 of 51)

1. Protein DDI1 homolog 2

SQQSHSSPGE ITSSPQGLDN PALLRDMLLA NPHELSLLKE RNPPLAEALL SGDLEKFSRV LVEQQQDRAR REQERIRLFS ADPFDLEAQA KIEEDIRQ

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4, Details 280 uM [U-13C; U-15N] hdd, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	hdd	[U-13C; U-15N]		280 uM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: -0.13 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.13 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.04 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.13 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 30 models in PDB: 5K57, Strand ID: A Detail

Release date

2016-08-07

Citation

Human DNA-Damage-Inducible 2 Protein Is Structurally and Functionally Distinct from Its Yeast Ortholog
Siva, M., Svoboda, M., Veverka, V., Trempe, J.F., Hofmann, K., Kozisek, M., Hexnerova, R., Sedlak, F., Belza, J., Brynda, J., Sacha, P., Hubalek, M., Starkova, J., Flaisigova, I., Konvalinka, J., Saskova, K.G.
Sci. Rep. (2016), 6, 30443-30443, PubMed 27461074 , DOI 10.1038/srep30443 , Abstract

Related entities 1. Protein DDI1 homolog 2, : 2 : 34 entities Detail

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4, Details 280 uM [U-13C; U-15N] hdd, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	hdd	[U-13C; U-15N]		280 uM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

2 3D CBCA(CO)NH

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4, Details 280 uM [U-13C; U-15N] hdd, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	hdd	[U-13C; U-15N]		280 uM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

3 3D HNCACB

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4, Details 280 uM [U-13C; U-15N] hdd, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	hdd	[U-13C; U-15N]		280 uM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

4 3D HNCO

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4, Details 280 uM [U-13C; U-15N] hdd, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	hdd	[U-13C; U-15N]		280 uM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

5 3D HN(CA)CO

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4, Details 280 uM [U-13C; U-15N] hdd, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	hdd	[U-13C; U-15N]		280 uM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

6 3D HCCH-TOCSY

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4, Details 280 uM [U-13C; U-15N] hdd, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	hdd	[U-13C; U-15N]		280 uM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

7 3D 1H-13C NOESY

Instrument

Bruker AvanceIII - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4, Details 280 uM [U-13C; U-15N] hdd, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	hdd	[U-13C; U-15N]		280 uM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

8 3D 1H-15N NOESY

Instrument

Bruker AvanceIII - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4, Details 280 uM [U-13C; U-15N] hdd, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	hdd	[U-13C; U-15N]		280 uM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_30097_5k57.nef
Input source #2: Coordindates	5k57.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--------
SQQSHSSPGEITSSPQGLDNPALLRDMLLANPHELSLLKERNPPLAEALLSGDLEKFSRVLVEQQQDRARREQERIRLFSADPFDLEAQAKIEEDIRQ
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SQQSHSSPGEITSSPQGLDNPALLRDMLLANPHELSLLKERNPPLAEALLSGDLEKFSRVLVEQQQDRARREQERIRLFSADPFDLEAQAKIEEDIRQ

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	98	0	0	100.0

Content subtype: combined_30097_5k57.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1086		99.0 (chain: A, length: 98)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	2763 (1)	noe	94.9 (chain: A, length: 98)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 98, Sequence coverage: 99.0%
- Total number of assignments
  - ¹H chemical shifts: 578
  - ¹³C chemical shifts: 405
  - ¹⁵N chemical shifts: 103
- 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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 98, Sequence coverage: 94.9%
- Total number of restraints: 2763
- Weight of restraints: 1.0 (2763)
- Potential type of restraints: square-well-parabolic (2763)
- Range of distance target values: 1.28, 3.16 (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

Keywords Ddi2, hydrolase