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BMRB: 19713

2MJA

Solution Structure of Domain-Swapped GLPG

Authors

Ghasriani, H., Kwok, J.K.C., Sherrat, A.R., Goto, N.K.

Assembly

Domain-Swapped GLPG

Entity

1. Domain-Swapped GLPG (polymer, Thiol state: not present), 63 monomers, 7150.987 × 2 Da Detail

MLMITSFANP RVAQAFVDYM ATQGVILTIQ QHNQSDVWLA DESQAERVRA ELARFLENPA DLE

Total weight

14301.974 Da

Max. entity weight

7150.987 Da

Source organism

Escherichia coli

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 83.6 %, Completeness (bb): 82.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	83.6 % (610 of 730)	92.0 % (346 of 376)	68.9 % (195 of 283)	97.2 % (69 of 71)
Backbone	82.4 % (308 of 374)	98.4 % (123 of 125)	67.0 % (126 of 188)	96.7 % (59 of 61)
Sidechain	87.1 % (364 of 418)	88.8 % (223 of 251)	83.4 % (131 of 157)	100.0 % (10 of 10)
Aromatic	50.0 % (27 of 54)	96.3 % (26 of 27)	0.0 % (0 of 26)	100.0 % (1 of 1)
Methyl	100.0 % (80 of 80)	100.0 % (40 of 40)	100.0 % (40 of 40)

1. Domain Swapped GLPG

MLMITSFANP RVAQAFVDYM ATQGVILTIQ QHNQSDVWLA DESQAERVRA ELARFLENPA DLE

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 25mM NaH2PO4, 150mM NaCl

#	Name	Isotope labeling	Type	Concentration
1	Domain Swapped GLPG	[U-100% 13C; U-100% 15N]		1 mM
2	NaH2PO4	natural abundance		25 mM
3	NaCl	natural abundance		150 mM
4	H2O	natural abundance		90 %
5	D2O	[U-100% 2H]		10 %

LACS Plot; CA

Referencing offset: -0.01 ppm, Outliers: 3 Detail

LACS Plot; CB

Referencing offset: -0.01 ppm, Outliers: 3 Detail

LACS Plot; HA

Referencing offset: -0.1 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2014-11-09

Citation

Micelle-catalyzed domain swapping in the GlpG rhomboid protease cytoplasmic domain
Ghasriani, H., Kwok, J.K.C., Sherrat, A.R., Foo, A.C.Y., Qureshi, T., Goto, N.K.
Biochemistry (2014), 53, 5907-5915, PubMed 25162988 , DOI 10.1021/bi500919v , Abstract

Related entities 1. Domain-Swapped GLPG, : 1 : 1 : 11 : 24 entities Detail

Interaction partners 1. Domain-Swapped GLPG, : 3 interactors Detail

More details for 3 interactors identified by 3 citations

Experiments performed 7 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 500 MHz Ottawa, Ontario.

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 25mM NaH2PO4, 150mM NaCl

#	Name	Isotope labeling	Type	Concentration
1	Domain Swapped GLPG	[U-100% 13C; U-100% 15N]		1 mM
2	NaH2PO4	natural abundance		25 mM
3	NaCl	natural abundance		150 mM
4	H2O	natural abundance		90 %
5	D2O	[U-100% 2H]		10 %

2 3D HNCO

Instrument

Varian INOVA - 500 MHz Ottawa, Ontario.

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 25mM NaH2PO4, 150mM NaCl

#	Name	Isotope labeling	Type	Concentration
1	Domain Swapped GLPG	[U-100% 13C; U-100% 15N]		1 mM
2	NaH2PO4	natural abundance		25 mM
3	NaCl	natural abundance		150 mM
4	H2O	natural abundance		90 %
5	D2O	[U-100% 2H]		10 %

3 3D HNCA

Instrument

Varian INOVA - 500 MHz Ottawa, Ontario.

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 25mM NaH2PO4, 150mM NaCl

#	Name	Isotope labeling	Type	Concentration
1	Domain Swapped GLPG	[U-100% 13C; U-100% 15N]		1 mM
2	NaH2PO4	natural abundance		25 mM
3	NaCl	natural abundance		150 mM
4	H2O	natural abundance		90 %
5	D2O	[U-100% 2H]		10 %

4 3D HNCACB

Instrument

Varian INOVA - 500 MHz Ottawa, Ontario.

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 25mM NaH2PO4, 150mM NaCl

#	Name	Isotope labeling	Type	Concentration
1	Domain Swapped GLPG	[U-100% 13C; U-100% 15N]		1 mM
2	NaH2PO4	natural abundance		25 mM
3	NaCl	natural abundance		150 mM
4	H2O	natural abundance		90 %
5	D2O	[U-100% 2H]		10 %

5 3D HCCH-TOCSY

Instrument

Varian INOVA - 500 MHz Ottawa, Ontario.

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 25mM NaH2PO4, 150mM NaCl

#	Name	Isotope labeling	Type	Concentration
1	Domain Swapped GLPG	[U-100% 13C; U-100% 15N]		1 mM
2	NaH2PO4	natural abundance		25 mM
3	NaCl	natural abundance		150 mM
4	H2O	natural abundance		90 %
5	D2O	[U-100% 2H]		10 %

6 3D 1H-13C NOESY aliphatic

Instrument

Varian INOVA - 500 MHz Ottawa, Ontario.

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 25mM NaH2PO4, 150mM NaCl

#	Name	Isotope labeling	Type	Concentration
1	Domain Swapped GLPG	[U-100% 13C; U-100% 15N]		1 mM
2	NaH2PO4	natural abundance		25 mM
3	NaCl	natural abundance		150 mM
4	H2O	natural abundance		90 %
5	D2O	[U-100% 2H]		10 %

7 3D 1H-15N NOESY

Instrument

Varian INOVA - 500 MHz Ottawa, Ontario.

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 25mM NaH2PO4, 150mM NaCl

#	Name	Isotope labeling	Type	Concentration
1	Domain Swapped GLPG	[U-100% 13C; U-100% 15N]		1 mM
2	NaH2PO4	natural abundance		25 mM
3	NaCl	natural abundance		150 mM
4	H2O	natural abundance		90 %
5	D2O	[U-100% 2H]		10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19713_2mja.nef
Input source #2: Coordindates	2mja.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---------
MLMITSFANPRVAQAFVDYMATQGVILTIQQHNQSDVWLADESQAERVRAELARFLENPADLEHHHHHH
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MLMITSFANPRVAQAFVDYMATQGVILTIQQHNQSDVWLADESQAERVRAELARFLENPADLEHHHHHH

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

--------10--------20--------30--------40--------50--------60---------
MLMITSFANPRVAQAFVDYMATQGVILTIQQHNQSDVWLADESQAERVRAELARFLENPADLEHHHHHH
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MLMITSFANPRVAQAFVDYMATQGVILTIQQHNQSDVWLADESQAERVRAELARFLENPADLEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	69	0	0	100.0
B	B	69	0	0	100.0

Content subtype: combined_19713_2mja.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	605		91.3 (chain: A, length: 69)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	2943 (1)	noe	91.3 (chain: A, length: 69), 91.3 (chain: B, length: 69)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	164 (164)	.	76.8 (chain: A, length: 69), 76.8 (chain: B, length: 69)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 69, Sequence coverage: 91.3%
- Total number of assignments
  - ¹H chemical shifts: 343
  - ¹³C chemical shifts: 193
  - ¹⁵N chemical shifts: 69
- 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

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 69, Sequence coverage: 91.3%
  - Entity_assembly_ID: B, Chain length: 69, Sequence coverage: 91.3%
- Total number of restraints: 2938
- Weight of restraints: 1.0 (2938)
- Potential type of restraints: upper-bound-parabolic (2938)
- Range of distance target values: 2.48, 5.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 69, Sequence coverage: 76.8%
  - Entity_assembly_ID: B, Chain length: 69, Sequence coverage: 76.8%
- Total number of restraints: 164
- Total number of restraints per polymer type: 164
- Weight of restraints: 1.0 (164)
- Potential type of restraints: square-well-parabolic (164)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

Keywords CELL MEMBRANE, CYTOSOL, DOMAIN SWAPPING, HYDROLASE, INTRAMEMBRANE PROTEASE, MEMBRANE PROTEIN, MICELLES, PEPTIDASE, RHOMBOID PROTEASE, SERINE PROTEASE