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BMRB: 18338

2LUW

C-terminal propeptide (PPc) region of vibrio extracellular metalloprotease

Authors

Assembly

PPc

Entity

1. PPc (polymer, Thiol state: all disulfide bound), 101 monomers, 10772.78 Da Detail

GNVLKNNTPV SNLTGNKGSE VFYTFTVDRN ATAVVSISGG SGDADLYLKA GSKPTTSSWD CRPYRYGNNE SCSVSAAPGT TYHVMIKGYS NYSGVTLKLQ Y

Formula weight

10772.78 Da

Source organism

Vibrio vulnificus

Exptl. method

Refine. method

DGSA-distance geometry simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.0 %, Completeness: 90.6 %, Completeness (bb): 96.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	90.6 % (997 of 1100)	93.1 % (523 of 562)	86.5 % (372 of 430)	94.4 % (102 of 108)
Backbone	96.7 % (578 of 598)	95.7 % (200 of 209)	97.3 % (284 of 292)	96.9 % (94 of 97)
Sidechain	86.0 % (509 of 592)	91.5 % (323 of 353)	78.1 % (178 of 228)	72.7 % (8 of 11)
Aromatic	34.0 % (34 of 100)	62.0 % (31 of 50)	4.1 % (2 of 49)	100.0 % (1 of 1)
Methyl	98.0 % (98 of 100)	98.0 % (49 of 50)	98.0 % (49 of 50)

1. C-terminal propeptide (PPc) region of vibrio extracellular metalloprotease

GNVLKNNTPV SNLTGNKGSE VFYTFTVDRN ATAVVSISGG SGDADLYLKA GSKPTTSSWD CRPYRYGNNE SCSVSAAPGT TYHVMIKGYS NYSGVTLKLQ Y

Show sample condition

Sample #1

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

#	Name	Isotope labeling	Type	Concentration
1	PPc protein	[U-100% 15N]		0.6 mM
2	HEPES (pH 7.0)	natural abundance		20 mM
3	Sodium chloride	natural abundance		100 mM
4	DTT	natural abundance		10 mM
5	NaN3	natural abundance		0.01 %
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

Sample #2

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

#	Name	Isotope labeling	Type	Concentration
8	PPc protein	[U-100% 13C; U-100% 15N]		0.6 mM
9	HEPES (pH 7.0)	natural abundance		20 mM
10	Sodium chloride	natural abundance		100 mM
11	DTT	natural abundance		10 mM
12	NaN3	natural abundance		0.01 %
13	H2O	natural abundance		90 %
14	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: 0.03 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: 0.03 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: -0.09 ppm, Outliers: 2 Detail

LACS Plot; CO

Referencing offset: 0.97 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2013-01-02

Citation

Solution structure and dynamics of C-terminal regulatory domain of Vibrio vulnificus extracellular metalloprotease
Yun, J., Kim, H., Park, J., Lee, J., Lee, W.
Biochem. Biophys. Res. Commun. (2013), 430, 541-546, PubMed 23228665 , DOI 10.1016/j.bbrc.2012.11.117 , Abstract

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

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DRX - 500 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	PPc protein	[U-100% 15N]		0.6 mM
2	HEPES (pH 7.0)	natural abundance		20 mM
3	Sodium chloride	natural abundance		100 mM
4	DTT	natural abundance		10 mM
5	NaN3	natural abundance		0.01 %
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

2 3D 1H-15N NOESY

Instrument

Bruker DRX - 500 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	PPc protein	[U-100% 15N]		0.6 mM
2	HEPES (pH 7.0)	natural abundance		20 mM
3	Sodium chloride	natural abundance		100 mM
4	DTT	natural abundance		10 mM
5	NaN3	natural abundance		0.01 %
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

3 3D 1H-13C NOESY

Instrument

Bruker DRX - 500 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
8	PPc protein	[U-100% 13C; U-100% 15N]		0.6 mM
9	HEPES (pH 7.0)	natural abundance		20 mM
10	Sodium chloride	natural abundance		100 mM
11	DTT	natural abundance		10 mM
12	NaN3	natural abundance		0.01 %
13	H2O	natural abundance		90 %
14	D2O	natural abundance		10 %

4 3D HNCACB

Instrument

Bruker DRX - 500 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
8	PPc protein	[U-100% 13C; U-100% 15N]		0.6 mM
9	HEPES (pH 7.0)	natural abundance		20 mM
10	Sodium chloride	natural abundance		100 mM
11	DTT	natural abundance		10 mM
12	NaN3	natural abundance		0.01 %
13	H2O	natural abundance		90 %
14	D2O	natural abundance		10 %

5 3D HBHA(CO)NH

Instrument

Bruker DRX - 500 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
8	PPc protein	[U-100% 13C; U-100% 15N]		0.6 mM
9	HEPES (pH 7.0)	natural abundance		20 mM
10	Sodium chloride	natural abundance		100 mM
11	DTT	natural abundance		10 mM
12	NaN3	natural abundance		0.01 %
13	H2O	natural abundance		90 %
14	D2O	natural abundance		10 %

6 3D HNCA

Instrument

Bruker DRX - 500 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
8	PPc protein	[U-100% 13C; U-100% 15N]		0.6 mM
9	HEPES (pH 7.0)	natural abundance		20 mM
10	Sodium chloride	natural abundance		100 mM
11	DTT	natural abundance		10 mM
12	NaN3	natural abundance		0.01 %
13	H2O	natural abundance		90 %
14	D2O	natural abundance		10 %

7 3D HNCO

Instrument

Bruker DRX - 500 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
8	PPc protein	[U-100% 13C; U-100% 15N]		0.6 mM
9	HEPES (pH 7.0)	natural abundance		20 mM
10	Sodium chloride	natural abundance		100 mM
11	DTT	natural abundance		10 mM
12	NaN3	natural abundance		0.01 %
13	H2O	natural abundance		90 %
14	D2O	natural abundance		10 %

8 3D HBHA(CO)NH

Instrument

Bruker DRX - 500 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
8	PPc protein	[U-100% 13C; U-100% 15N]		0.6 mM
9	HEPES (pH 7.0)	natural abundance		20 mM
10	Sodium chloride	natural abundance		100 mM
11	DTT	natural abundance		10 mM
12	NaN3	natural abundance		0.01 %
13	H2O	natural abundance		90 %
14	D2O	natural abundance		10 %

9 3D HCCH-TOCSY

Instrument

Bruker DRX - 500 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
8	PPc protein	[U-100% 13C; U-100% 15N]		0.6 mM
9	HEPES (pH 7.0)	natural abundance		20 mM
10	Sodium chloride	natural abundance		100 mM
11	DTT	natural abundance		10 mM
12	NaN3	natural abundance		0.01 %
13	H2O	natural abundance		90 %
14	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_18338_2luw.nef
Input source #2: Coordindates	2luw.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
GNVLKNNTPVSNLTGNKGSEVFYTFTVDRNATAVVSISGGSGDADLYLKAGSKPTTSSWDCRPYRYGNNESCSVSAAPGTTYHVMIKGYSNYSGVTLKLQ
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GNVLKNNTPVSNLTGNKGSEVFYTFTVDRNATAVVSISGGSGDADLYLKAGSKPTTSSWDCRPYRYGNNESCSVSAAPGTTYHVMIKGYSNYSGVTLKLQ

-
Y
|
Y

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	101	0	0	100.0

Content subtype: combined_18338_2luw.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_of_PPc_region	Warning	999		99.0 (chain: A, length: 101)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	34 (1)	hbond	33.7 (chain: A, length: 101)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	104 (104)	.	80.2 (chain: A, length: 101)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_of_PPc_region
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 101, Sequence coverage: 99.0%
- Total number of assignments
  - ¹H chemical shifts: 529
  - ¹³C chemical shifts: 368
  - 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

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_3
- Status: OK
- Experiment type: hbond
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 101, Sequence coverage: 33.7%
- Total number of restraints: 34
- Weight of restraints: 1.0 (34)
- Potential type of restraints: upper-bound-parabolic (34)
- Range of distance target values: 2.0, 3.0 (Å)
- Histogram of 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: 101, Sequence coverage: 80.2%
- 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
  - Chain_ID: A