BMRBj - BMREntryMaster

	Total	¹H	¹³C	¹⁵N
All	82.1 % (1136 of 1383)	78.5 % (560 of 713)	83.6 % (460 of 550)	96.7 % (116 of 120)
Backbone	94.4 % (670 of 710)	93.9 % (229 of 244)	94.1 % (332 of 353)	96.5 % (109 of 113)
Sidechain	73.1 % (573 of 784)	70.6 % (331 of 469)	76.3 % (235 of 308)	100.0 % (7 of 7)
Aromatic	57.1 % (64 of 112)	60.7 % (34 of 56)	52.7 % (29 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: 0.16 ppm, Outliers: 1 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: 0.16 ppm, Outliers: 1 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: 1 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: 0.46 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2RUF, 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 (reduced 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_11562_2ruf.nef
Input source #2: Coordindates	2ruf.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
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_11562_2ruf.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1108		95.9 (chain: A, length: 121)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	2654 (1)	noe	95.9 (chain: A, length: 121)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	74 (1)	hbond	45.5 (chain: A, length: 121)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	178 (178)	.	86.0 (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: 95.9%
- Total number of assignments
  - ¹H chemical shifts: 545
  - ¹³C chemical shifts: 448
  - ¹⁵N chemical shifts: 115
- 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	713	545	76.4
¹³C chemical shifts	550	448	81.5
¹⁵N chemical shifts	122	115	94.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	244	229	93.9
¹³C chemical shifts	242	220	90.9
¹⁵N chemical shifts	113	108	95.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	469	316	67.4
¹³C chemical shifts	308	228	74.0
¹⁵N chemical shifts	9	7	77.8

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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	56	28	50.0
¹³C chemical shifts	55	26	47.3
¹⁵N chemical shifts	1	1	100.0

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: 95.9%
- Total number of restraints: 2654
- Weight of restraints: 1.0 (2654)
- Potential type of restraints: square-well-parabolic (2654)
- Range of distance target values: 2.29, 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: 121, Sequence coverage: 45.5%
  - Total number of restraints: 74
  - Weight of restraints: 1.0 (74)
  - Potential type of restraints: square-well-parabolic (74)
  - Range of distance target values: 1.3, 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: 86.0%
- Total number of restraints: 178
- Total number of restraints per polymer type: 178
- Weight of restraints: 1.0 (178)
- Potential type of restraints: square-well-parabolic (178)
- 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: 11562

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Chemical shift reference

Chemical shift reference

Chemical shift reference

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

Experiments performed 6 experiments Detail

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Sample

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Sample

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NMR combined restraints 5 contents Detail