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Found 1 Document (0.679 seconds)

BMRB: 16109

2KDB

Solution Structure of human ubiquitin-like domain of Herpud2_9_85, Northeast Structural Genomics Consortium (NESG) target HT53A

Authors

Wu, B., Yee, A., Fares, C., Lemak, A., Gutmanas, A., Doherty, R., Semesi, A., Dhe-Paganon, S., Arrowsmith, C.

Assembly

Herpud2 9 85

Entity

1. Herpud2 9 85 (polymer, Thiol state: all free), 99 monomers, 11547.06 Da Detail

MGSSHHHHHH SSGRENLYFQ GHPVTLIIKA PNQKYSDQTI SCFLNWTVGK LKTHLSNVYP SKPLTKDQRL VYSGRLLPDH LQLKDILRKQ DEYHMVHLV

Formula weight

11547.06 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 81.8 %, Completeness: 78.2 %, Completeness (bb): 77.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	78.2 % (943 of 1206)	80.2 % (505 of 630)	76.9 % (362 of 471)	72.4 % (76 of 105)
Backbone	77.1 % (450 of 584)	77.3 % (153 of 198)	77.7 % (227 of 292)	74.5 % (70 of 94)
Sidechain	79.7 % (571 of 716)	81.5 % (352 of 432)	77.7 % (212 of 273)	63.6 % (7 of 11)
Aromatic	50.0 % (58 of 116)	62.1 % (36 of 58)	36.8 % (21 of 57)	100.0 % (1 of 1)
Methyl	100.0 % (104 of 104)	100.0 % (52 of 52)	100.0 % (52 of 52)

1. humna ubiquitin-like domain of Herp

MGSSHHHHHH SSGRENLYFQ GHPVTLIIKA PNQKYSDQTI SCFLNWTVGK LKTHLSNVYP SKPLTKDQRL VYSGRLLPDH LQLKDILRKQ DEYHMVHLV

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	humna ubiquitin-like domain of Herp	[U-100% 13C; U-100% 15N]	0.5 mM
2	TRIS	[U-100% 2H]	10 mM
3	sodium chloride	natural abundance	300 mM
4	sodium azide	natural abundance	0.01 %
5	benzamidine	natural abundance	10 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
8	humna ubiquitin-like domain of Herp	[U-100% 13C; U-100% 15N]	0.5 mM
9	TRIS	[U-100% 2H]	10 mM
10	sodium chloride	natural abundance	300 mM
11	sodium azide	natural abundance	0.01 %
12	benzamidine	natural abundance	10 mM
13	D2O	natural abundance	100 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
14	humna ubiquitin-like domain of Herp	[U-7% 13C; U-100% 15N]	0.5 mM
15	TRIS	[U-100% 2H]	10 mM
16	sodium chloride	natural abundance	300 mM
17	sodium azide	natural abundance	0.01 %
18	benzamidine	natural abundance	10 mM
19	H2O	natural abundance	90 %
20	D2O	natural abundance	10 %

LACS Plot; CA

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

Referencing offset: -0.27 ppm, Outliers: 2 Detail

LACS Plot; CB

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

Referencing offset: -0.27 ppm, Outliers: 2 Detail

LACS Plot; HA

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

Referencing offset: -0.01 ppm, Outliers: 5 Detail

LACS Plot; CO

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

Referencing offset: -1.73 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2KDB, Strand ID: A Detail

Release date

2009-05-25

Citation

Structure of human homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 2 (Herpud2 or Herp)
Doherty, R.S., Wu, B., Fares, C., Lemak, A., Gutmanas, A., Semesi, A., Yee, A., Arrowsmith, C.H., Dhe-Paganon, S.
Not known

Related entities 1. Herpud2 9 85, : 1 : 18 entities Detail

Experiments performed 11 experiments Detail

1 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	humna ubiquitin-like domain of Herp	[U-100% 13C; U-100% 15N]	0.5 mM
2	TRIS	[U-100% 2H]	10 mM
3	sodium chloride	natural abundance	300 mM
4	sodium azide	natural abundance	0.01 %
5	benzamidine	natural abundance	10 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

2 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	humna ubiquitin-like domain of Herp	[U-100% 13C; U-100% 15N]	0.5 mM
2	TRIS	[U-100% 2H]	10 mM
3	sodium chloride	natural abundance	300 mM
4	sodium azide	natural abundance	0.01 %
5	benzamidine	natural abundance	10 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

3 3D HBHA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	humna ubiquitin-like domain of Herp	[U-100% 13C; U-100% 15N]	0.5 mM
2	TRIS	[U-100% 2H]	10 mM
3	sodium chloride	natural abundance	300 mM
4	sodium azide	natural abundance	0.01 %
5	benzamidine	natural abundance	10 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

4 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	humna ubiquitin-like domain of Herp	[U-100% 13C; U-100% 15N]	0.5 mM
2	TRIS	[U-100% 2H]	10 mM
3	sodium chloride	natural abundance	300 mM
4	sodium azide	natural abundance	0.01 %
5	benzamidine	natural abundance	10 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

5 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	humna ubiquitin-like domain of Herp	[U-100% 13C; U-100% 15N]	0.5 mM
2	TRIS	[U-100% 2H]	10 mM
3	sodium chloride	natural abundance	300 mM
4	sodium azide	natural abundance	0.01 %
5	benzamidine	natural abundance	10 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

6 3D CCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	humna ubiquitin-like domain of Herp	[U-100% 13C; U-100% 15N]	0.5 mM
2	TRIS	[U-100% 2H]	10 mM
3	sodium chloride	natural abundance	300 mM
4	sodium azide	natural abundance	0.01 %
5	benzamidine	natural abundance	10 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

7 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	humna ubiquitin-like domain of Herp	[U-100% 13C; U-100% 15N]	0.5 mM
2	TRIS	[U-100% 2H]	10 mM
3	sodium chloride	natural abundance	300 mM
4	sodium azide	natural abundance	0.01 %
5	benzamidine	natural abundance	10 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

8 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	humna ubiquitin-like domain of Herp	[U-100% 13C; U-100% 15N]	0.5 mM
2	TRIS	[U-100% 2H]	10 mM
3	sodium chloride	natural abundance	300 mM
4	sodium azide	natural abundance	0.01 %
5	benzamidine	natural abundance	10 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

9 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
8	humna ubiquitin-like domain of Herp	[U-100% 13C; U-100% 15N]	0.5 mM
9	TRIS	[U-100% 2H]	10 mM
10	sodium chloride	natural abundance	300 mM
11	sodium azide	natural abundance	0.01 %
12	benzamidine	natural abundance	10 mM
13	D2O	natural abundance	100 %

10 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	humna ubiquitin-like domain of Herp	[U-100% 13C; U-100% 15N]	0.5 mM
2	TRIS	[U-100% 2H]	10 mM
3	sodium chloride	natural abundance	300 mM
4	sodium azide	natural abundance	0.01 %
5	benzamidine	natural abundance	10 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

11 2D 1H-13C HSQC

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
14	humna ubiquitin-like domain of Herp	[U-7% 13C; U-100% 15N]	0.5 mM
15	TRIS	[U-100% 2H]	10 mM
16	sodium chloride	natural abundance	300 mM
17	sodium azide	natural abundance	0.01 %
18	benzamidine	natural abundance	10 mM
19	H2O	natural abundance	90 %
20	D2O	natural abundance	10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_16109_2kdb.nef
Input source #2: Coordindates	2kdb.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-------
MGSSHHHHHHSSGRENLYFQGHPVTLIIKAPNQKYSDQTISCFLNWTVGKLKTHLSNVYPSKPLTKDQRLVYSGRLLPDHLQLKDILRKQDEYHMVHLV
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGSSHHHHHHSSGRENLYFQGHPVTLIIKAPNQKYSDQTISCFLNWTVGKLKTHLSNVYPSKPLTKDQRLVYSGRLLPDHLQLKDILRKQDEYHMVHLV
--------10--------20--------30--------40--------50--------60--------70--------80--------90---------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	99	0	0	100.0

Content subtype: combined_16109_2kdb.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	902		77.8 (chain: A, length: 99)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	2766 (1)	noe	76.8 (chain: A, length: 99)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	62 (1)	hbond	40.4 (chain: A, length: 99)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	112 (112)	.	76.8 (chain: A, length: 99)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 99, Sequence coverage: 77.8%
- Total number of assignments
  - ¹H chemical shifts: 480
  - ¹³C chemical shifts: 349
  - ¹⁵N chemical shifts: 73
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	630	480	76.2
¹³C chemical shifts	471	349	74.1
¹⁵N chemical shifts	109	73	67.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	198	145	73.2
¹³C chemical shifts	198	143	72.2
¹⁵N chemical shifts	94	67	71.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	432	335	77.5
¹³C chemical shifts	273	206	75.5
¹⁵N chemical shifts	15	6	40.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	54	50	92.6
¹³C chemical shifts	54	50	92.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	58	32	55.2
¹³C chemical shifts	57	21	36.8
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 99, Sequence coverage: 76.8%
- Total number of restraints: 2766
- Weight of restraints: 1.0 (2766)
- Potential type of restraints: square-well-parabolic (2766)
- Range of distance target values: 2.25, 3.9 (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: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 99, Sequence coverage: 40.4%
  - Total number of restraints: 62
  - Weight of restraints: 1.0 (62)
  - Potential type of restraints: square-well-parabolic (62)
  - Range of distance target values: 2.05, 3.0 (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_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 99, Sequence coverage: 76.8%
- Total number of restraints: 112
- Total number of restraints per polymer type: 112
- Weight of restraints: 1.0 (112)
- Potential type of restraints: square-well-parabolic (112)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

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Found 1 Document (0.679 seconds)

BMRB: 16109

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Herpud2 9 85, : 1 : 18 entities Detail

Experiments performed 11 experiments Detail

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NMR combined restraints 5 contents Detail