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Found 1 Document (1.871 seconds)

BMRB: 19689

2MZV

Resonance assignments of a phytocystatin from Sesamum indicum L.

Authors

Deli, I., Hu, Y., Chyan, C.

Assembly

SiCYS

Entity

1. SiCYS (polymer, Thiol state: not present), 199 monomers, 22350.94 Da Detail

MATLGGVHDS NSNPDTHSLA RFAVDQHNTK ENGLLELVRV VEAREQVVAG TLHHLVLEVL DAGKKKLYEA KIWVKPWMDF KQLQEFKHVR DVPSFTSSDL GAKTDDQVSG WRPVPVHDPV VQDAAHHAIK TIQERSNSLF PYELSEVVHA NAEVVDTSAK FDMLLKVKRG GKEEKYKVEV HKSTEEGGFN LKKVDLDHS

Formula weight

22350.94 Da

Source organism

Escherichia coli

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 90.9 %, Completeness (bb): 98.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	90.9 % (2107 of 2318)	92.6 % (1112 of 1201)	87.4 % (794 of 908)	96.2 % (201 of 209)
Backbone	98.0 % (1156 of 1180)	97.3 % (391 of 402)	98.1 % (575 of 586)	99.0 % (190 of 192)
Sidechain	85.5 % (1134 of 1326)	90.2 % (721 of 799)	78.8 % (402 of 510)	64.7 % (11 of 17)
Aromatic	37.6 % (67 of 178)	75.3 % (67 of 89)	0.0 % (0 of 86)	0.0 % (0 of 3)
Methyl	99.6 % (229 of 230)	100.0 % (115 of 115)	99.1 % (114 of 115)

1. SiCYS

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	SiCYS	[U-100% 13C; U-100% 15N]		80 uM

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	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.05 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	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.05 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	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.08 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	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.3 ppm, Outliers: 3 Detail

Protein Blocks Logo

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

Release date

2014-04-10

Citation

Resonance assignments and secondary structure of a phytocystatin from Sesamum indicum
Irene, D., Sung, F., Huang, J., Lin, T., Chen, Y., Chyan, C.
Biomol. NMR Assign. (2015), 9, 309-311, PubMed 25673506 , DOI 10.1007/s12104-015-9598-y , Abstract

Related entities 1. SiCYS, : 1 : 18 entities Detail

Experiments performed 8 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19689_2mzv.nef
Input source #2: Coordindates	2mzv.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
MATLGGVHDSNSNPDTHSLARFAVDQHNTKENGLLELVRVVEAREQVVAGTLHHLVLEVLDAGKKKLYEAKIWVKPWMDFKQLQEFKHVRDVPSFTSSDL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MATLGGVHDSNSNPDTHSLARFAVDQHNTKENGLLELVRVVEAREQVVAGTLHHLVLEVLDAGKKKLYEAKIWVKPWMDFKQLQEFKHVRDVPSFTSSDL

-------110-------120-------130-------140-------150-------160-------170-------180-------190---------
GAKTDDQVSGWRPVPVHDPVVQDAAHHAIKTIQERSNSLFPYELSEVVHANAEVVDTSAKFDMLLKVKRGGKEEKYKVEVHKSTEEGGFNLKKVDLDHS
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GAKTDDQVSGWRPVPVHDPVVQDAAHHAIKTIQERSNSLFPYELSEVVHANAEVVDTSAKFDMLLKVKRGGKEEKYKVEVHKSTEEGGFNLKKVDLDHS

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	199	0	0	100.0

Content subtype: combined_19689_2mzv.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	2114		100.0 (chain: A, length: 199)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	3849 (1)	noe	99.5 (chain: A, length: 199)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	226 (226)	.	72.9 (chain: A, length: 199)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 199, Sequence coverage: 100.0%
- Total number of assignments
  - ¹³C chemical shifts: 788
  - ¹H chemical shifts: 1125
  - ¹⁵N chemical shifts: 201
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	908	788	86.8
¹H chemical shifts	1201	1125	93.7
¹⁵N chemical shifts	216	201	93.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	398	387	97.2
¹H chemical shifts	402	396	98.5
¹⁵N chemical shifts	192	190	99.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	510	401	78.6
¹H chemical shifts	799	729	91.2
¹⁵N chemical shifts	24	11	45.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	118	114	96.6
¹H chemical shifts	118	115	97.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	86	0	0.0
¹H chemical shifts	89	66	74.2
¹⁵N chemical shifts	3	0	0.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 199, Sequence coverage: 99.5%
- Total number of restraints: 3841
- Weight of restraints: 1.0 (3841)
- Potential type of restraints: square-well-parabolic (3841)
- Range of distance target values: 1.92, 3.7 (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

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 199, Sequence coverage: 72.9%
- Total number of restraints: 226
- Total number of restraints per polymer type: 226
- Weight of restraints: 1.0 (226)
- Potential type of restraints: square-well-parabolic (226)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

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Found 1 Document (1.871 seconds)

BMRB: 19689

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. SiCYS, : 1 : 18 entities Detail

Experiments performed 8 experiments Detail

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NMR combined restraints 4 contents Detail