BMRBj - BMREntryMaster

Found 1 Document (0.737 seconds)

BMRB: 30131

5KQC

Identification and structural characterization of LytU

Authors

Tossavainen, H., Raulinaitis, V., 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 × 2 Da

Total weight

16378.738 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: 97.9 %, Completeness: 86.2 %, Completeness (bb): 80.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	86.2 % (1467 of 1701)	94.6 % (839 of 887)	74.7 % (494 of 661)	87.6 % (134 of 153)
Backbone	80.1 % (686 of 856)	91.4 % (276 of 302)	69.2 % (288 of 416)	88.4 % (122 of 138)
Sidechain	93.3 % (906 of 971)	96.2 % (563 of 585)	89.2 % (331 of 371)	80.0 % (12 of 15)
Aromatic	82.3 % (158 of 192)	97.9 % (94 of 96)	66.0 % (62 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, 1.25 mM zinc chloride, 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
1	LytU	[U-13C; U-15N]	0.5 mM
2	bisTris buffer		20 mM
3	zinc chloride		1.25 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: -0.07 ppm, Outliers: 1 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: -0.07 ppm, Outliers: 1 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: -0.01 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 15 models in PDB: 5KQC, 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 12 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, 1.25 mM zinc chloride, 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
1	LytU	[U-13C; U-15N]	0.5 mM
2	bisTris buffer		20 mM
3	zinc chloride		1.25 mM

2 2D 1H-13C HSQC aliphatic

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	LytU	[U-13C; U-15N]	0.5 mM
2	bisTris buffer		20 mM
3	zinc chloride		1.25 mM

3 2D 1H-13C HSQC aromatic

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	LytU	[U-13C; U-15N]	0.5 mM
2	bisTris buffer		20 mM
3	zinc chloride		1.25 mM

4 3D HNCACB

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	LytU	[U-13C; U-15N]	0.5 mM
2	bisTris buffer		20 mM
3	zinc chloride		1.25 mM

5 3D HN(CO)CACB

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	LytU	[U-13C; U-15N]	0.5 mM
2	bisTris buffer		20 mM
3	zinc chloride		1.25 mM

6 2D (HB)CB(CGCD)HD

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	LytU	[U-13C; U-15N]	0.5 mM
2	bisTris buffer		20 mM
3	zinc chloride		1.25 mM

7 3D HCCH-COSY

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	LytU	[U-13C; U-15N]	0.5 mM
2	bisTris buffer		20 mM
3	zinc chloride		1.25 mM

8 3D H(CCO)NH

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	LytU	[U-13C; U-15N]	0.5 mM
2	bisTris buffer		20 mM
3	zinc chloride		1.25 mM

9 3D C(CO)NH

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	LytU	[U-13C; U-15N]	0.5 mM
2	bisTris buffer		20 mM
3	zinc chloride		1.25 mM

10 2D (HB)CB(CGCDCE)HE

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	LytU	[U-13C; U-15N]	0.5 mM
2	bisTris buffer		20 mM
3	zinc chloride		1.25 mM

11 3D 1H-13C NOESY

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	LytU	[U-13C; U-15N]	0.5 mM
2	bisTris buffer		20 mM
3	zinc chloride		1.25 mM

12 3D 1H-15N NOESY

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	LytU	[U-13C; U-15N]	0.5 mM
2	bisTris buffer		20 mM
3	zinc chloride		1.25 mM

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_30131_5kqc.nef
Input source #2: Coordindates	5kqc.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_30131_5kqc.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	1441		97.2 (chain: A, length: 145)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	3697 (1)	noe	94.5 (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: 97.2%
- Total number of assignments
  - ¹H chemical shifts: 841
  - ¹³C chemical shifts: 465
  - ¹⁵N chemical shifts: 135
- 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)
76	HIS	HD1	11.553
87	THR	HG1	6.183
98	THR	HG1	5.682
120	HIS	HE2	11.071
125	HIS	HD1	11.363
159	HIS	HE2	12.928

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	887	835	94.1
¹³C chemical shifts	661	465	70.3
¹⁵N chemical shifts	159	135	84.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	302	275	91.1
¹³C chemical shifts	290	139	47.9
¹⁵N chemical shifts	138	119	86.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	585	560	95.7
¹³C chemical shifts	371	326	87.9
¹⁵N chemical shifts	21	16	76.2

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	93	96.9
¹³C chemical shifts	94	59	62.8
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: 94.5%
- Total number of restraints: 3684
- Weight of restraints: 1.0 (3684)
- Potential type of restraints: upper-bound-parabolic (3684)
- Range of distance target values: 2.45, 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

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.737 seconds)

BMRB: 30131

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 12 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 3 contents Detail