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BMRB: 19751

2MK4

Solution structure of ORF2

Authors

Miyakawa, T., Kobayashi, H., Tashiro, M., Yamanaka, H., Tanokura, M.

Assembly

ORF2

Entity

1. ORF2 (polymer, Thiol state: not present), 133 monomers, 13988.58 Da Detail

GPVQESVTMD GKQYSTIEVN GQTYLIPDNG SKKRVARSLD SKVPQQTLRR GDVLMQGAAS PELTVSGTLL VEADDASAKA LATRHGLNFK QSSGGIALLE AKPGTDLNAI ATKLKSEGVN VQIELSGAEQ QPK

Formula weight

13988.58 Da

Source organism

Aeromonas sobria

Exptl. method

Refine. method

DGSA-distance geometry simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.5 %, Completeness: 81.2 %, Completeness (bb): 87.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	81.2 % (1191 of 1466)	83.6 % (638 of 763)	77.2 % (433 of 561)	84.5 % (120 of 142)
Backbone	87.0 % (684 of 786)	91.9 % (251 of 273)	81.1 % (313 of 386)	94.5 % (120 of 127)
Sidechain	77.4 % (619 of 800)	79.0 % (387 of 490)	78.6 % (232 of 295)	0.0 % (0 of 15)
Aromatic	0.0 % (0 of 30)	0.0 % (0 of 15)	0.0 % (0 of 15)
Methyl	85.6 % (137 of 160)	91.3 % (73 of 80)	80.0 % (64 of 80)

1. entity

GPVQESVTMD GKQYSTIEVN GQTYLIPDNG SKKRVARSLD SKVPQQTLRR GDVLMQGAAS PELTVSGTLL VEADDASAKA LATRHGLNFK QSSGGIALLE AKPGTDLNAI ATKLKSEGVN VQIELSGAEQ QPK

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	ORF2	[U-99% 13C; U-99% 15N]		0.9 mM
2	MOPS	natural abundance		18 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: -0.1 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: -0.1 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: -0.03 ppm, Outliers: 2 Detail

LACS Plot; CO

Referencing offset: 0.19 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2MK4, Strand ID: A Detail

Release date

2015-03-22

Citation

Structural Basis for Action of the External Chaperone for a Propeptide-deficient Serine Protease from Aeromonas sobria
Kobayashi, H., Yoshida, T., Miyakawa, T., Tashiro, M., Okamoto, K., Yamanaka, H., Tanokura, M., Tsuge, H.
J. Biol. Chem. (2015), 290, 11130-11143, PubMed 25784551 , DOI 10.1074/jbc.M114.622852 , Abstract

Related entities 1. ORF2, : 1 : 1 : 2 entities Detail

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	ORF2	[U-99% 13C; U-99% 15N]		0.9 mM
2	MOPS	natural abundance		18 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

2 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	ORF2	[U-99% 13C; U-99% 15N]		0.9 mM
2	MOPS	natural abundance		18 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

3 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	ORF2	[U-99% 13C; U-99% 15N]		0.9 mM
2	MOPS	natural abundance		18 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

4 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	ORF2	[U-99% 13C; U-99% 15N]		0.9 mM
2	MOPS	natural abundance		18 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

5 3D C(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	ORF2	[U-99% 13C; U-99% 15N]		0.9 mM
2	MOPS	natural abundance		18 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

6 3D HBHA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	ORF2	[U-99% 13C; U-99% 15N]		0.9 mM
2	MOPS	natural abundance		18 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

7 3D H(CCO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	ORF2	[U-99% 13C; U-99% 15N]		0.9 mM
2	MOPS	natural abundance		18 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

8 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	ORF2	[U-99% 13C; U-99% 15N]		0.9 mM
2	MOPS	natural abundance		18 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

9 3D 1H-13C NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	ORF2	[U-99% 13C; U-99% 15N]		0.9 mM
2	MOPS	natural abundance		18 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

10 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	ORF2	[U-99% 13C; U-99% 15N]		0.9 mM
2	MOPS	natural abundance		18 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19751_2mk4.nef
Input source #2: Coordindates	2mk4.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-------
GPVQESVTMDGKQYSTIEVNGQTYLIPDNGSKKRVARSLDSKVPQQTLRRGDVLMQGAASPELTVSGTLLVEADDASAKALATRHGLNFKQSSGGIALLE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GPVQESVTMDGKQYSTIEVNGQTYLIPDNGSKKRVARSLDSKVPQQTLRRGDVLMQGAASPELTVSGTLLVEADDASAKALATRHGLNFKQSSGGIALLE
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

100-------110-------120-------130
AKPGTDLNAIATKLKSEGVNVQIELSGAEQQPK
|||||||||||||||||||||||||||||||||
AKPGTDLNAIATKLKSEGVNVQIELSGAEQQPK
-------110-------120-------130---

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	133	0	0	100.0

Content subtype: combined_19751_2mk4.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1181		97.0 (chain: A, length: 133)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	1857 (1)	noe	80.5 (chain: A, length: 133)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	104 (104)	.	44.4 (chain: A, length: 133)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 133, Sequence coverage: 97.0%
- Total number of assignments
  - ¹H chemical shifts: 646
  - ¹³C chemical shifts: 416
  - ¹⁵N chemical shifts: 119
- 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: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 133, Sequence coverage: 80.5%
- Total number of restraints: 1857
- Weight of restraints: 1.0 (1857)
- Potential type of restraints: upper-bound-parabolic (1857)
- Range of distance target values: 2.4, 5.5 (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_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 133, Sequence coverage: 44.4%
- Total number of restraints: 104
- Total number of restraints per polymer type: 104
- Weight of restraints: 1.0 (104)
- Potential type of restraints: square-well-parabolic (104)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue

Keywords PROTEIN