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Found 1 Document (0.556 seconds)

BMRB: 25745

5ABK

Structure of the N-terminal domain of the metalloprotease PrtV from Vibrio cholerae

Authors

Persson, C., Mayzel, M., Edwin, A., Wai, S.N., Ohman, A., Sauer-eriksson, A.E., Karlsson, G.

Assembly

N-terminal domain of the metalloprotease PrtV from Vibrio cholerae

Entity

1. N-terminal domain of the metalloprotease PrtV from Vibrio cholerae (polymer, Thiol state: not present), 84 monomers, 9343.744 Da Detail

GAMAQTPIDL GVVNEDKLIE MLVRTGQIPA DASDVDKRIA LERYLEEKIR SGFKGDAQFG KKALEQRAKI LKVIDKQKGP HKAR

Formula weight

9343.744 Da

Source organism

Vibrio cholerae

Exptl. method

solution NMR

Refine. method

CYANA 2.1

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 89.6 %, Completeness (bb): 99.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.6 % (892 of 996)	85.8 % (453 of 528)	94.2 % (359 of 381)	92.0 % (80 of 87)
Backbone	99.2 % (494 of 498)	98.3 % (169 of 172)	100.0 % (245 of 245)	98.8 % (80 of 81)
Sidechain	82.6 % (475 of 575)	79.8 % (284 of 356)	89.7 % (191 of 213)	0.0 % (0 of 6)
Aromatic	37.5 % (12 of 32)	75.0 % (12 of 16)	0.0 % (0 of 16)
Methyl	100.0 % (98 of 98)	100.0 % (49 of 49)	100.0 % (49 of 49)

1. METALLOPROTEASE

GAMAQTPIDL GVVNEDKLIE MLVRTGQIPA DASDVDKRIA LERYLEEKIR SGFKGDAQFG KKALEQRAKI LKVIDKQKGP HKAR

Show sample condition

Sample

Solvent system 20mM Pi, pH7.0 10%D2O, Pressure 1 atm, Temperature 283.000 K, pH 7.000, Details 0.7 mM PrtV

#	Name	Isotope labeling	Type	Concentration
1	METALLOPROTEASE	[U-13C; U-15N]		0.7 mM
2	Pi	natural abundance		20 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	0.0 ppm	external	indirect	1.0

Referencing offset: 2.8 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	0.0 ppm	external	indirect	1.0

Referencing offset: 2.8 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	0.0 ppm	external	indirect	1.0

Referencing offset: 0.27 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	0.0 ppm	external	indirect	1.0

Referencing offset: 2.87 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 5ABK, Strand ID: A Detail

Release date

2015-08-23

Citation

Structure of the N-terminal domain of the metalloprotease PrtV from Vibrio cholerae
Edwin, A., Mayzel, M., Persson, C., Wai, S.N., Ohman, A., Karlsson, G., Sauer-eriksson, A.E.
Protein Sci. (2015), 24, 2076-2080, PubMed 26434928 , DOI 10.1002/pro.2815 , Abstract

Related entities 1. N-terminal domain of the metalloprotease PrtV from Vibrio cholerae, : 1 entities Detail

Experiments performed 2 experiments Detail

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_25745_5abk.nef
Input source #2: Coordindates	5abk.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----
GAMAQTPIDLGVVNEDKLIEMLVRTGQIPADASDVDKRIALERYLEEKIRSGFKGDAQFGKKALEQRAKILKVIDKQKGPHKAR
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GAMAQTPIDLGVVNEDKLIEMLVRTGQIPADASDVDKRIALERYLEEKIRSGFKGDAQFGKKALEQRAKILKVIDKQKGPHKAR

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	84	0	0	100.0

Content subtype: combined_25745_5abk.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list	Warning	885		98.8 (chain: A, length: 84)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	879 (1)	noe	98.8 (chain: A, length: 84)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 84, Sequence coverage: 98.8%
- Total number of assignments
  - ¹H chemical shifts: 449
  - ¹³C chemical shifts: 357
  - ¹⁵N chemical shifts: 79
- 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 (%)
¹H chemical shifts	528	449	85.0
¹³C chemical shifts	381	357	93.7
¹⁵N chemical shifts	93	79	84.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	172	165	95.9
¹³C chemical shifts	168	166	98.8
¹⁵N chemical shifts	81	79	97.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	356	284	79.8
¹³C chemical shifts	213	191	89.7
¹⁵N chemical shifts	12	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	51	50	98.0
¹³C chemical shifts	51	50	98.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	16	12	75.0
¹³C chemical shifts	16	0	0.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 84, Sequence coverage: 98.8%
- Total number of restraints: 879
- Weight of restraints: 1.0 (879)
- Potential type of restraints: upper-bound-parabolic (879)
- Range of distance target values: 3.03, 7.5 (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

Keywords HYDROLASE, Metalloprotease, N-terminal domain, NMR, PrtV, Vibrio Cholerae

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Found 1 Document (0.556 seconds)

BMRB: 25745

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. N-terminal domain of the metalloprotease PrtV from Vibrio cholerae, : 1 entities Detail

Experiments performed 2 experiments Detail

Instrument

Sample

Instrument

Sample

NMR combined restraints 3 contents Detail