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Found 1 Document (0.675 seconds)

BMRB: 30130

5KQB

Identification and structural characterization of LytU

Authors

Raulinaitis, V., Tossavainen, H., Permi, P.

Assembly

Peptidase M23 (E.C.3.4.24.75)

Entity

1. Peptidase M23 (E.C.3.4.24.75), entity 1 (polymer, Thiol state: not present), 145 monomers, 16247.92 Da Detail

GSKWEDFFRG SRITETFGKY QHSPFDGKHY GIDFALPKGT PIKAPTNGKV TRIFNNELGG KVLQIAEDNG EYHQWYLHLD KYNVKVGDRV KAGDIIAYSG NTGIQTTGAH LHFQRMKGGV GNAYAEDPKP FIDQLPDGER SLYDL

2. Peptidase M23 (E.C.3.4.24.75), entity ZN (non-polymer), 65.409 Da

Total weight

16313.329 Da

Max. entity weight

16247.92 Da

Entity Connection

na 4 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:HIS29:NE2	2:ZN1:ZN
2	na	sing	1:ASP33:OD1	2:ZN1:ZN
3	na	sing	1:ASP33:OD2	2:ZN1:ZN
4	na	sing	1:HIS112:ND1	2:ZN1:ZN

Source organism

Staphylococcus aureus

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.3 %, Completeness: 87.1 %, Completeness (bb): 82.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	87.1 % (1481 of 1701)	94.8 % (841 of 887)	75.9 % (502 of 661)	90.2 % (138 of 153)
Backbone	82.5 % (706 of 856)	94.4 % (285 of 302)	70.7 % (294 of 416)	92.0 % (127 of 138)
Sidechain	92.8 % (901 of 971)	95.0 % (556 of 585)	90.0 % (334 of 371)	73.3 % (11 of 15)
Aromatic	78.1 % (150 of 192)	94.8 % (91 of 96)	60.6 % (57 of 94)	100.0 % (2 of 2)
Methyl	100.0 % (128 of 128)	100.0 % (64 of 64)	100.0 % (64 of 64)

1. entity 1

GSKWEDFFRG SRITETFGKY QHSPFDGKHY GIDFALPKGT PIKAPTNGKV TRIFNNELGG KVLQIAEDNG EYHQWYLHLD KYNVKVGDRV KAGDIIAYSG NTGIQTTGAH LHFQRMKGGV GNAYAEDPKP FIDQLPDGER SLYDL

Show sample condition

Sample

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 0.5 mM [U-13C; U-15N] LytU, 20 mM bisTris buffer, 0.5 mM zinc chloride, 93% H2O/7% D2O

#	Name	Isotope labeling	Type	Concentration
1	Bis-Tris buffer			20 mM
2	LytU	[U-13C; U-15N]		0.5 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl carbons	46.01 ppm	internal	indirect	0.2514495
¹H	water	protons	4.67 ppm	internal	direct	1.0
¹⁵N	liquid anhydrous ammonia	nitrogen	117.79 ppm	internal	indirect	0.1013291

Referencing offset: -0.14 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl carbons	46.01 ppm	internal	indirect	0.2514495
¹H	water	protons	4.67 ppm	internal	direct	1.0
¹⁵N	liquid anhydrous ammonia	nitrogen	117.79 ppm	internal	indirect	0.1013291

Referencing offset: -0.14 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl carbons	46.01 ppm	internal	indirect	0.2514495
¹H	water	protons	4.67 ppm	internal	direct	1.0
¹⁵N	liquid anhydrous ammonia	nitrogen	117.79 ppm	internal	indirect	0.1013291

Referencing offset: -0.02 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 15 models in PDB: 5KQB, Strand ID: A Detail

Release date

2016-11-10

Citation

Identification and structural characterization of LytU, a unique peptidoglycan endopeptidase from the lysostaphin family
Raulinaitis, V., Tossavainen, H., Aitio, O., Juuti, J.T., Hiramatsu, K., Kontinen, V., Permi, P.
Sci. Rep. (2017), 7, 6020-6020, PubMed 28729697 , DOI 10.1038/s41598-017-06135-w , Abstract

Related entities 1. Peptidase M23 (E.C.3.4.24.75), entity 1, : 1 : 1 : 1 : 14 entities Detail

Experiments performed 15 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 0.5 mM [U-13C; U-15N] LytU, 20 mM bisTris buffer, 0.5 mM zinc chloride, 93% H2O/7% D2O

#	Name	Isotope labeling	Type	Concentration
1	Bis-Tris buffer			20 mM
2	LytU	[U-13C; U-15N]		0.5 mM

2 2D 1H-13C HSQC aliphatic

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	Bis-Tris buffer			20 mM
2	LytU	[U-13C; U-15N]		0.5 mM

3 2D 1H-13C HSQC aromatic

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	Bis-Tris buffer			20 mM
2	LytU	[U-13C; U-15N]		0.5 mM

4 3D HNCA

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	Bis-Tris buffer			20 mM
2	LytU	[U-13C; U-15N]		0.5 mM

5 3D HNCACB

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	Bis-Tris buffer			20 mM
2	LytU	[U-13C; U-15N]		0.5 mM

6 3D C(CO)NH

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	Bis-Tris buffer			20 mM
2	LytU	[U-13C; U-15N]		0.5 mM

7 3D HN(CO)CACB

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	Bis-Tris buffer			20 mM
2	LytU	[U-13C; U-15N]		0.5 mM

8 3D HN(CO)CA

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	Bis-Tris buffer			20 mM
2	LytU	[U-13C; U-15N]		0.5 mM

9 3D H(CCO)NH

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	Bis-Tris buffer			20 mM
2	LytU	[U-13C; U-15N]		0.5 mM

10 3D HBHA(CO)NH

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	Bis-Tris buffer			20 mM
2	LytU	[U-13C; U-15N]		0.5 mM

11 3D 1H-15N NOESY

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	Bis-Tris buffer			20 mM
2	LytU	[U-13C; U-15N]		0.5 mM

12 3D HCCH-COSY

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	Bis-Tris buffer			20 mM
2	LytU	[U-13C; U-15N]		0.5 mM

13 3D 1H-13C NOESY

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	Bis-Tris buffer			20 mM
2	LytU	[U-13C; U-15N]		0.5 mM

14 2D (HB)CB(CGCDCE)HE

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	Bis-Tris buffer			20 mM
2	LytU	[U-13C; U-15N]		0.5 mM

15 2D (HB)CB(CGCD)HD

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	Bis-Tris buffer			20 mM
2	LytU	[U-13C; U-15N]		0.5 mM

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_30130_5kqb.nef
Input source #2: Coordindates	5kqb.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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:29:HIS:NE2	2:1:ZN:ZN	unknown	unknown	n/a
1:33:ASP:OD1	2:1:ZN:ZN	unknown	unknown	n/a
1:33:ASP:OD2	2:1:ZN:ZN	unknown	unknown	n/a
1:112:HIS:ND1	2:1:ZN:ZN	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	ZN	ZINC ION	None

Sequence alignments

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

--50-------60--------70--------80--------90-------100-------110-------120-------130-------140-------
GSKWEDFFRGSRITETFGKYQHSPFDGKHYGIDFALPKGTPIKAPTNGKVTRIFNNELGGKVLQIAEDNGEYHQWYLHLDKYNVKVGDRVKAGDIIAYSG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSKWEDFFRGSRITETFGKYQHSPFDGKHYGIDFALPKGTPIKAPTNGKVTRIFNNELGGKVLQIAEDNGEYHQWYLHLDKYNVKVGDRVKAGDIIAYSG
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

150-------160-------170-------180-------190--
NTGIQTTGAHLHFQRMKGGVGNAYAEDPKPFIDQLPDGERSLYDL
|||||||||||||||||||||||||||||||||||||||||||||
NTGIQTTGAHLHFQRMKGGVGNAYAEDPKPFIDQLPDGERSLYDL
-------110-------120-------130-------140-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	145	0	0	100.0

Content subtype: combined_30130_5kqb.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1463		99.3 (chain: A, length: 145)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	3901 (1)	noe	96.6 (chain: A, length: 145)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 145, Sequence coverage: 99.3%
- Total number of assignments
  - ¹H chemical shifts: 851
  - ¹³C chemical shifts: 474
  - ¹⁵N chemical shifts: 138
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- Tautomeric state of HIS
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
87	THR	HG1	6.192
98	THR	HG1	5.643
120	HIS	HE2	11.091
120	HIS	NE2	163.423
157	HIS	HD1	12.304
159	HIS	HE2	12.958
159	HIS	NE2	167.713

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	887	846	95.4
¹³C chemical shifts	661	474	71.7
¹⁵N chemical shifts	159	136	85.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	302	285	94.4
¹³C chemical shifts	290	143	49.3
¹⁵N chemical shifts	138	124	89.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	585	561	95.9
¹³C chemical shifts	371	331	89.2
¹⁵N chemical shifts	21	12	57.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	65	65	100.0
¹³C chemical shifts	65	65	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	96	91	94.8
¹³C chemical shifts	94	55	58.5
¹⁵N chemical shifts	2	2	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 145, Sequence coverage: 96.6%
- Total number of restraints: 3883
- Weight of restraints: 1.0 (3883)
- Potential type of restraints: upper-bound-parabolic (3883)
- Range of distance target values: 2.51, 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
    None
- Distance restraints on contact map

Keywords LytU, hydrolase, lysostaphin, peptidoglycan, zinc

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Found 1 Document (0.675 seconds)

BMRB: 30130

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Peptidase M23 (E.C.3.4.24.75), entity 1, : 1 : 1 : 1 : 14 entities Detail

Experiments performed 15 experiments Detail

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NMR combined restraints 3 contents Detail