BMRBj - BMREntryMaster

	Total	¹H	¹³C	¹⁵N
All	74.3 % (837 of 1126)	78.7 % (448 of 569)	63.3 % (286 of 452)	98.1 % (103 of 105)
Backbone	81.8 % (507 of 620)	95.4 % (207 of 217)	66.3 % (201 of 303)	99.0 % (99 of 100)
Sidechain	70.3 % (421 of 599)	68.5 % (241 of 352)	72.7 % (176 of 242)	80.0 % (4 of 5)
Aromatic	7.7 % (6 of 78)	10.3 % (4 of 39)	5.1 % (2 of 39)
Methyl	87.7 % (128 of 146)	90.4 % (66 of 73)	84.9 % (62 of 73)

1. entity

PLTRPYLGFR VAVGRDSSGC TTLSIQEVTQ TYTGSNGGAD LMGPAFAAGL RVGDQLVRFA GYTVTELAAF NTVVARHVRP SASIPVVFSR DGVVMSATIV VGELE

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	100 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	direct	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	direct	0.0

Referencing offset: 0.8 ppm, Outliers: 7 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	direct	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	direct	0.0

Referencing offset: 0.8 ppm, Outliers: 7 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	direct	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	direct	0.0

Referencing offset: -0.06 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2NB4, Strand ID: A Detail

Release date

2016-02-21

Citation

Solution structure of Q388A3 PDZ domain from Trypanosoma brucei
Mei, S., Dong, Y., Zhang, J., Zhang, X., Tu, X.
J. Struct. Biol. (2016), 194, 214-217, PubMed 26917351 , DOI 10.1016/j.jsb.2016.02.018 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 25816 released on 2015-10-04
Title Solution structure of PDZ domain

Related entities 1. Q388A3 PDZ domain, : 1 : 1 : 10 entities Detail

Experiments performed 1 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25961_2nb4.nef
Input source #2: Coordindates	2nb4.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
PLTRPYLGFRVAVGRDSSGCTTLSIQEVTQTYTGSNGGADLMGPAFAAGLRVGDQLVRFAGYTVTELAAFNTVVARHVRPSASIPVVFSRDGVVMSATIV
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PLTRPYLGFRVAVGRDSSGCTTLSIQEVTQTYTGSNGGADLMGPAFAAGLRVGDQLVRFAGYTVTELAAFNTVVARHVRPSASIPVVFSRDGVVMSATIV

-----
VGELE
|||||
VGELE

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	105	0	0	100.0

Content subtype: combined_25961_2nb4.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	820		100.0 (chain: A, length: 105)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	888 (1)	noe	99.0 (chain: A, length: 105)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	28 (1)	hbond	19.0 (chain: A, length: 105)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	183 (183)	.	99.0 (chain: A, length: 105)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 105, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 442
  - ¹³C chemical shifts: 276
  - ¹⁵N chemical shifts: 102
- 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	569	442	77.7
¹³C chemical shifts	452	276	61.1
¹⁵N chemical shifts	113	102	90.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	217	206	94.9
¹³C chemical shifts	210	103	49.0
¹⁵N chemical shifts	100	98	98.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	352	236	67.0
¹³C chemical shifts	242	173	71.5
¹⁵N chemical shifts	13	4	30.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	75	66	88.0
¹³C chemical shifts	75	62	82.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	39	0	0.0
¹³C chemical shifts	39	0	0.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 105, Sequence coverage: 99.0%
- Total number of restraints: 888
- Weight of restraints: 1.0 (888)
- Potential type of restraints: square-well-parabolic (888)
- Range of distance target values: 2.7, 4.15 (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: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 105, Sequence coverage: 19.0%
  - Total number of restraints: 28
  - Weight of restraints: 1.0 (28)
  - Potential type of restraints: square-well-parabolic (28)
  - Range of distance target values: 2.5, 3.5 (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: 105, Sequence coverage: 99.0%
- Total number of restraints: 183
- Total number of restraints per polymer type: 183
- Weight of restraints: 1.0 (183)
- Potential type of restraints: square-well-parabolic (183)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords PDZ NMR

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BMRB: 25961

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. Q388A3 PDZ domain, : 1 : 1 : 10 entities Detail

Experiments performed 1 experiments Detail

Instrument

Sample

NMR combined restraints 5 contents Detail