BMRBj - BMREntryMaster

	Total	¹H	¹³C	¹⁵N
All	81.6 % (1128 of 1383)	79.7 % (568 of 713)	81.6 % (449 of 550)	92.5 % (111 of 120)
Backbone	93.2 % (662 of 710)	94.3 % (230 of 244)	92.6 % (327 of 353)	92.9 % (105 of 113)
Sidechain	72.6 % (569 of 784)	72.1 % (338 of 469)	73.1 % (225 of 308)	85.7 % (6 of 7)
Aromatic	50.9 % (57 of 112)	51.8 % (29 of 56)	49.1 % (27 of 55)	100.0 % (1 of 1)
Methyl	91.2 % (135 of 148)	91.9 % (68 of 74)	90.5 % (67 of 74)

1. PDI

GPLGSEGPVT VVVAKNYNEI VLDDTKDVLI EFYAPWCGHC KALAPKYEEL GALYAKSEFK DRVVIAKVDA TANDVPDEIQ GFPTIKLYPA GAKGQPVTYS GSRTVEDLIK FIAENGKYKA A

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	PDI	[U-15N]	protein	0.1 mM
2	sodium phosphate	natural abundance	buffer	10 mM
3	potassium chloride	natural abundance	salt	100 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	natural abundance	solvent	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
6	PDI	[U-13C; U-15N]	protein	0.1 mM
7	sodium phosphate	natural abundance	buffer	10 mM
8	potassium chloride	natural abundance	salt	100 mM
9	D2O	natural abundance	solvent	100 %

LACS Plot; CA

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

Referencing offset: 0.04 ppm, Outliers: 3 Detail

LACS Plot; CB

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

Referencing offset: 0.04 ppm, Outliers: 3 Detail

LACS Plot; HA

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

Referencing offset: -0.01 ppm, Outliers: 3 Detail

LACS Plot; CO

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

Referencing offset: 0.43 ppm, Outliers: 4 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2RUE, Strand ID: A Detail

Release date

2015-05-17

Citation

1H , 13C and 15N Assigned Chemical Shifts for PDI
Inagaki, K., Satoh, T., Kato, K.
Not known

Related entities 1. a' domain of Protein Disulfide Isomerase (oxidized form), : 1 : 3 : 4 : 349 entities Detail

Experiments performed 6 experiments Detail

1 2D 1H-15N HSQC

Instrument

JEOL ECA - 920 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	PDI	[U-15N]	protein	0.1 mM
2	sodium phosphate	natural abundance	buffer	10 mM
3	potassium chloride	natural abundance	salt	100 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	natural abundance	solvent	10 %

2 3D 1H-15N NOESY

Instrument

JEOL ECA - 920 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	PDI	[U-15N]	protein	0.1 mM
2	sodium phosphate	natural abundance	buffer	10 mM
3	potassium chloride	natural abundance	salt	100 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	natural abundance	solvent	10 %

3 2D 1H-13C HSQC aliphatic

Instrument

JEOL ECA - 920 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
6	PDI	[U-13C; U-15N]	protein	0.1 mM
7	sodium phosphate	natural abundance	buffer	10 mM
8	potassium chloride	natural abundance	salt	100 mM
9	D2O	natural abundance	solvent	100 %

4 2D 1H-13C HSQC aromatic

Instrument

JEOL ECA - 920 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
6	PDI	[U-13C; U-15N]	protein	0.1 mM
7	sodium phosphate	natural abundance	buffer	10 mM
8	potassium chloride	natural abundance	salt	100 mM
9	D2O	natural abundance	solvent	100 %

5 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
6	PDI	[U-13C; U-15N]	protein	0.1 mM
7	sodium phosphate	natural abundance	buffer	10 mM
8	potassium chloride	natural abundance	salt	100 mM
9	D2O	natural abundance	solvent	100 %

6 2D 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
6	PDI	[U-13C; U-15N]	protein	0.1 mM
7	sodium phosphate	natural abundance	buffer	10 mM
8	potassium chloride	natural abundance	salt	100 mM
9	D2O	natural abundance	solvent	100 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_11561_2rue.nef
Input source #2: Coordindates	2rue.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:37:CYS:SG	A:40:CYS:SG	oxidized, CA 61.828, CB 44.865 ppm	oxidized, CA 63.571, CB 33.644 ppm	2.031

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
GPLGSEGPVTVVVAKNYNEIVLDDTKDVLIEFYAPWCGHCKALAPKYEELGALYAKSEFKDRVVIAKVDATANDVPDEIQGFPTIKLYPAGAKGQPVTYS
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GPLGSEGPVTVVVAKNYNEIVLDDTKDVLIEFYAPWCGHCKALAPKYEELGALYAKSEFKDRVVIAKVDATANDVPDEIQGFPTIKLYPAGAKGQPVTYS

-------110-------120-
GSRTVEDLIKFIAENGKYKAA
|||||||||||||||||||||
GSRTVEDLIKFIAENGKYKAA

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	121	0	0	100.0

Content subtype: combined_11561_2rue.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1135		99.2 (chain: A, length: 121)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1868 (1)	noe	94.2 (chain: A, length: 121)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	66 (1)	hbond	40.5 (chain: A, length: 121)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	182 (182)	.	95.9 (chain: A, length: 121)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 121, Sequence coverage: 99.2%
- Total number of assignments
  - ¹H chemical shifts: 576
  - ¹³C chemical shifts: 449
  - ¹⁵N chemical shifts: 110
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
86	LYS	NZ	124.432
99	TYR	HH	6.498

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	713	575	80.6
¹³C chemical shifts	550	449	81.6
¹⁵N chemical shifts	122	109	89.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	244	234	95.9
¹³C chemical shifts	242	224	92.6
¹⁵N chemical shifts	113	103	91.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	469	341	72.7
¹³C chemical shifts	308	225	73.1
¹⁵N chemical shifts	9	6	66.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	74	69	93.2
¹³C chemical shifts	74	67	90.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	56	29	51.8
¹³C chemical shifts	55	27	49.1
¹⁵N chemical shifts	1	1	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 121, Sequence coverage: 94.2%
- Total number of restraints: 1868
- Weight of restraints: 1.0 (1868)
- Potential type of restraints: square-well-parabolic (1868)
- Range of distance target values: 2.35, 4.08 (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: 121, Sequence coverage: 40.5%
  - Total number of restraints: 66
  - Weight of restraints: 1.0 (66)
  - Potential type of restraints: square-well-parabolic (66)
  - Range of distance target values: 2.2, 3.2 (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: 121, Sequence coverage: 95.9%
- Total number of restraints: 182
- Total number of restraints per polymer type: 182
- Weight of restraints: 1.0 (182)
- Potential type of restraints: square-well-parabolic (182)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords DISULFIDE BOND, ENDOPLASMIC RETICULUM, ISOMERASE, REDOX-ACTIVE CENTER, THIOREDOXIN FOLD

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BMRB: 11561

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Sample #2

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Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. a' domain of Protein Disulfide Isomerase (oxidized form), : 1 : 3 : 4 : 349 entities Detail

Experiments performed 6 experiments Detail

Instrument

Sample

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Sample

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NMR combined restraints 5 contents Detail