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BMRB: 19987

2MPK

Characterization and structure of the MIT1 domain of a chitin synthase from the Oomycete Saprolegnia monoica

Authors

Bulone, V., Szpryngiel, S., Brown, C., Ye, W.

Assembly

MIT1 domain of a chitin synthase

Entity

1. MIT1 domain of a chitin synthase (polymer, Thiol state: not present), 74 monomers, 8513.544 Da Detail

MGTIDDAFRA IERAIQAENE GRYREALKHF LDGGEMIVTA AEKEASQKVR NLLLHKGKEV LEWAEHLAEW ILEH

Formula weight

8513.544 Da

Source organism

Saprolegnia monoica

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.6 %, Completeness: 87.4 %, Completeness (bb): 94.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	87.4 % (763 of 873)	89.6 % (407 of 454)	83.2 % (282 of 339)	92.5 % (74 of 80)
Backbone	94.4 % (419 of 444)	98.0 % (150 of 153)	90.3 % (196 of 217)	98.6 % (73 of 74)
Sidechain	82.1 % (409 of 498)	85.4 % (257 of 301)	79.1 % (151 of 191)	16.7 % (1 of 6)
Aromatic	27.9 % (19 of 68)	55.9 % (19 of 34)	0.0 % (0 of 32)	0.0 % (0 of 2)
Methyl	100.0 % (88 of 88)	100.0 % (44 of 44)	100.0 % (44 of 44)

1. SmChs MIT1

MGTIDDAFRA IERAIQAENE GRYREALKHF LDGGEMIVTA AEKEASQKVR NLLLHKGKEV LEWAEHLAEW ILEH

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
1	SmChs_MIT1	[U-100% 13C; U-100% 15N]		0.3 ~ 1.0 mM
2	D2O	natural abundance		10 %
3	sodium phosphate	natural abundance		50 mM
4	sodium chloride	natural abundance		150 mM
5	H2O	natural abundance		90 %

Protein Blocks Logo

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

Release date

2015-05-25

Citation

Structural and functional characterization of the microtubule interacting and trafficking domains of two oomycete chitin synthases
Bulone, V., Maler, L., Brown, C., Szpryngiel, S., KUANG, G., SRIVASTAVA, V., Ye, W., Tu, Y.
FEBS J. (2016), PubMed 27363606 , DOI 10.1111/febs.13794 , Abstract

Related entities 1. MIT1 domain of a chitin synthase, : 1 : 39 entities Detail

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz triple-resonance probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
1	SmChs_MIT1	[U-100% 13C; U-100% 15N]		0.3 ~ 1.0 mM
2	D2O	natural abundance		10 %
3	sodium phosphate	natural abundance		50 mM
4	sodium chloride	natural abundance		150 mM
5	H2O	natural abundance		90 %

2 3D HNCO

Instrument

Bruker Avance - 600 MHz triple-resonance probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
1	SmChs_MIT1	[U-100% 13C; U-100% 15N]		0.3 ~ 1.0 mM
2	D2O	natural abundance		10 %
3	sodium phosphate	natural abundance		50 mM
4	sodium chloride	natural abundance		150 mM
5	H2O	natural abundance		90 %

3 3D HNCA

Instrument

Bruker Avance - 600 MHz triple-resonance probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
1	SmChs_MIT1	[U-100% 13C; U-100% 15N]		0.3 ~ 1.0 mM
2	D2O	natural abundance		10 %
3	sodium phosphate	natural abundance		50 mM
4	sodium chloride	natural abundance		150 mM
5	H2O	natural abundance		90 %

4 3D HNCACB

Instrument

Bruker Avance - 600 MHz triple-resonance probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
1	SmChs_MIT1	[U-100% 13C; U-100% 15N]		0.3 ~ 1.0 mM
2	D2O	natural abundance		10 %
3	sodium phosphate	natural abundance		50 mM
4	sodium chloride	natural abundance		150 mM
5	H2O	natural abundance		90 %

5 3D HN(CO)CA

Instrument

Bruker Avance - 600 MHz triple-resonance probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
1	SmChs_MIT1	[U-100% 13C; U-100% 15N]		0.3 ~ 1.0 mM
2	D2O	natural abundance		10 %
3	sodium phosphate	natural abundance		50 mM
4	sodium chloride	natural abundance		150 mM
5	H2O	natural abundance		90 %

6 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz triple-resonance probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
1	SmChs_MIT1	[U-100% 13C; U-100% 15N]		0.3 ~ 1.0 mM
2	D2O	natural abundance		10 %
3	sodium phosphate	natural abundance		50 mM
4	sodium chloride	natural abundance		150 mM
5	H2O	natural abundance		90 %

7 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz triple-resonance probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
1	SmChs_MIT1	[U-100% 13C; U-100% 15N]		0.3 ~ 1.0 mM
2	D2O	natural abundance		10 %
3	sodium phosphate	natural abundance		50 mM
4	sodium chloride	natural abundance		150 mM
5	H2O	natural abundance		90 %

8 3D 1H-13C NOESY

Instrument

Bruker Avance - 600 MHz triple-resonance probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5

#	Name	Isotope labeling	Type	Concentration
1	SmChs_MIT1	[U-100% 13C; U-100% 15N]		0.3 ~ 1.0 mM
2	D2O	natural abundance		10 %
3	sodium phosphate	natural abundance		50 mM
4	sodium chloride	natural abundance		150 mM
5	H2O	natural abundance		90 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19987_2mpk.nef
Input source #2: Coordindates	2mpk.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----
MGTIDDAFRAIERAIQAENEGRYREALKHFLDGGEMIVTAAEKEASQKVRNLLLHKGKEVLEWAEHLAEWILEH
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGTIDDAFRAIERAIQAENEGRYREALKHFLDGGEMIVTAAEKEASQKVRNLLLHKGKEVLEWAEHLAEWILEH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	74	0	0	100.0

Content subtype: combined_19987_2mpk.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	757		98.6 (chain: A, length: 74)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	1871 (1)	noe	98.6 (chain: A, length: 74)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	118 (118)	.	87.8 (chain: A, length: 74)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 74, Sequence coverage: 98.6%
- Total number of assignments
  - ¹H chemical shifts: 406
  - ¹³C chemical shifts: 278
  - ¹⁵N chemical shifts: 73
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 74, Sequence coverage: 98.6%
- Total number of restraints: 1862
- Weight of restraints: 1.0 (1862)
- Potential type of restraints: upper-bound-parabolic (1862)
- Range of distance target values: 2.79, 6.02 (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: DYANA/DIANA_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 74, Sequence coverage: 87.8%
- Total number of restraints: 118
- Total number of restraints per polymer type: 118
- Weight of restraints: 1.0 (118)
- Potential type of restraints: square-well-parabolic (118)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords MIT domain, NMR, Oomycete, Saprolegnia, carbohydrate synthase, microtubule interacting and trafficking domain, protein, solution structure, three-helix bundle, transferase