BMRBj - BMREntryMaster

Found 1 Document (0.613 seconds)

BMRB: 34121

5NMY

NMR solution structure of lysostaphin

Authors

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

Assembly

Lysostaphin (E.C.3.4.24.75)

Entity

1. Lysostaphin (E.C.3.4.24.75), entity 1 (polymer, Thiol state: not present), 245 monomers, 26844.78 Da Detail

GSHEHSAQWL NNYKKGYGYG PYPLGINGGM HYGVDFFMNI GTPVKAISSG KIVEAGWSNY GGGNQIGLIE NDGVHRQWYM HLSKYNVKVG DYVKAGQIIG WSGSTGYSTA PHLHFQRMVN SFSNSTAQDP MPFLKSAGYG KAGGTVTPTP NTGWKTNKYG TLYKSESASF TPNTDIITRT TGPFRSMPQS GVLKAGQTIH YDEVMKQDGH VWVGYTGNSG QRIYLPVRTW NKSTNTLGVL WGTIK

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

Total weight

26910.188 Da

Max. entity weight

26844.78 Da

Source organism

Staphylococcus simulans

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.8 %, Completeness: 88.3 %, Completeness (bb): 84.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	88.3 % (2481 of 2810)	95.9 % (1391 of 1451)	76.9 % (840 of 1092)	93.6 % (250 of 267)
Backbone	84.5 % (1222 of 1446)	95.1 % (489 of 514)	73.5 % (514 of 699)	94.0 % (219 of 233)
Sidechain	92.4 % (1453 of 1573)	95.7 % (897 of 937)	87.4 % (526 of 602)	88.2 % (30 of 34)
Aromatic	80.6 % (266 of 330)	96.4 % (159 of 165)	63.1 % (99 of 157)	100.0 % (8 of 8)
Methyl	96.8 % (211 of 218)	97.2 % (106 of 109)	96.3 % (105 of 109)

1. entity 1

Show sample condition

Sample #1

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 0.36 mM [U-13C; U-15N] lysostaphin, 20 mM Bis-Tris, 0.36 mM ZnCl2, 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
1	lysostaphin	[U-13C; U-15N]	0.36 mM
2	Bis-Tris	natural abundance	20 mM
3	ZnCl2	natural abundance	0.36 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 0.47 mM [U-13C; U-15N] lysostaphin, 20 mM Bis-Tris, 0.36 mM ZnCl2, 100% D2O

#	Name	Isotope labeling	Concentration
4	lysostaphin	[U-13C; U-15N]	0.47 mM
5	Bis-Tris	natural abundance	20 mM
6	ZnCl2	natural abundance	0.36 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl carbons	0.0 ppm	na	indirect	0.2514495
¹H	water	protons	4.67 ppm	internal	direct	1.0
¹⁵N	liquid anhydrous ammonia	nitrogen	0.0 ppm	na	indirect	0.1013291

Referencing offset: -1.4 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	0.0 ppm	na	indirect	0.2514495
¹H	water	protons	4.67 ppm	internal	direct	1.0
¹⁵N	liquid anhydrous ammonia	nitrogen	0.0 ppm	na	indirect	0.1013291

Referencing offset: -1.4 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	0.0 ppm	na	indirect	0.2514495
¹H	water	protons	4.67 ppm	internal	direct	1.0
¹⁵N	liquid anhydrous ammonia	nitrogen	0.0 ppm	na	indirect	0.1013291

Referencing offset: -0.06 ppm, Outliers: 1 Detail

Release date

2017-04-10

Citation

Structural and Functional Insights Into Lysostaphin-Substrate Interaction
Tossavainen, H., Raulinaitis, V., Kauppinen, L., Pentikainen, U., Maaheimo, H., Permi, P.
Front. Mol. Biosci. (2018), 5, 60-60, PubMed 30018958 , DOI 10.3389/fmolb.2018.00060 , Abstract

Related entities 1. Lysostaphin (E.C.3.4.24.75), entity 1, : 1 : 5 entities Detail

Experiments performed 14 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 0.36 mM [U-13C; U-15N] lysostaphin, 20 mM Bis-Tris, 0.36 mM ZnCl2, 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
1	lysostaphin	[U-13C; U-15N]	0.36 mM
2	Bis-Tris	natural abundance	20 mM
3	ZnCl2	natural abundance	0.36 mM

2 2D 1H-13C HSQC aliphatic

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	lysostaphin	[U-13C; U-15N]	0.36 mM
2	Bis-Tris	natural abundance	20 mM
3	ZnCl2	natural abundance	0.36 mM

3 2D 1H-13C HSQC aromatic

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	lysostaphin	[U-13C; U-15N]	0.36 mM
2	Bis-Tris	natural abundance	20 mM
3	ZnCl2	natural abundance	0.36 mM

4 3D HNCACB

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	lysostaphin	[U-13C; U-15N]	0.36 mM
2	Bis-Tris	natural abundance	20 mM
3	ZnCl2	natural abundance	0.36 mM

5 3D CBCA(CO)NH

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	lysostaphin	[U-13C; U-15N]	0.36 mM
2	Bis-Tris	natural abundance	20 mM
3	ZnCl2	natural abundance	0.36 mM

6 3D 1H-15N NOESY

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	lysostaphin	[U-13C; U-15N]	0.36 mM
2	Bis-Tris	natural abundance	20 mM
3	ZnCl2	natural abundance	0.36 mM

7 3D HBHA(CO)NH

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	lysostaphin	[U-13C; U-15N]	0.36 mM
2	Bis-Tris	natural abundance	20 mM
3	ZnCl2	natural abundance	0.36 mM

8 3D C(CO)NH

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	lysostaphin	[U-13C; U-15N]	0.36 mM
2	Bis-Tris	natural abundance	20 mM
3	ZnCl2	natural abundance	0.36 mM

9 3D H(CCO)NH

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	lysostaphin	[U-13C; U-15N]	0.36 mM
2	Bis-Tris	natural abundance	20 mM
3	ZnCl2	natural abundance	0.36 mM

10 2D (HB)CB(CGCDCE)HE

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	lysostaphin	[U-13C; U-15N]	0.36 mM
2	Bis-Tris	natural abundance	20 mM
3	ZnCl2	natural abundance	0.36 mM

11 2D (HB)CB(CGCD)HD

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	lysostaphin	[U-13C; U-15N]	0.36 mM
2	Bis-Tris	natural abundance	20 mM
3	ZnCl2	natural abundance	0.36 mM

12 3D 1H-13C NOESY aliphatic

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 0.47 mM [U-13C; U-15N] lysostaphin, 20 mM Bis-Tris, 0.36 mM ZnCl2, 100% D2O

#	Name	Isotope labeling	Concentration
4	lysostaphin	[U-13C; U-15N]	0.47 mM
5	Bis-Tris	natural abundance	20 mM
6	ZnCl2	natural abundance	0.36 mM

13 3D HCCH-COSY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 0.47 mM [U-13C; U-15N] lysostaphin, 20 mM Bis-Tris, 0.36 mM ZnCl2, 100% D2O

#	Name	Isotope labeling	Concentration
4	lysostaphin	[U-13C; U-15N]	0.47 mM
5	Bis-Tris	natural abundance	20 mM
6	ZnCl2	natural abundance	0.36 mM

14 3D 1H-13C NOESY aromatic

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 0.47 mM [U-13C; U-15N] lysostaphin, 20 mM Bis-Tris, 0.36 mM ZnCl2, 100% D2O

#	Name	Isotope labeling	Concentration
4	lysostaphin	[U-13C; U-15N]	0.47 mM
5	Bis-Tris	natural abundance	20 mM
6	ZnCl2	natural abundance	0.36 mM

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_34121_5nmy.nef
Input source #2: Coordindates	5nmy.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)
1:31:HIS:NE2	2:1:ZN:ZN	unknown	unknown	n/a
1:35:ASP:OD1	2:1:ZN:ZN	unknown	unknown	n/a
1:114: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	Distance restraints

Sequence alignments

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

-250-----260-------270-------280-------290-------300-------310-------320-------330-------340-------3
GSHEHSAQWLNNYKKGYGYGPYPLGINGGMHYGVDFFMNIGTPVKAISSGKIVEAGWSNYGGGNQIGLIENDGVHRQWYMHLSKYNVKVGDYVKAGQIIG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSHEHSAQWLNNYKKGYGYGPYPLGINGGMHYGVDFFMNIGTPVKAISSGKIVEAGWSNYGGGNQIGLIENDGVHRQWYMHLSKYNVKVGDYVKAGQIIG
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

50-------360-------370-------380-------390-------400-------410-------420-------430-------440-------4
WSGSTGYSTAPHLHFQRMVNSFSNSTAQDPMPFLKSAGYGKAGGTVTPTPNTGWKTNKYGTLYKSESASFTPNTDIITRTTGPFRSMPQSGVLKAGQTIH
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
WSGSTGYSTAPHLHFQRMVNSFSNSTAQDPMPFLKSAGYGKAGGTVTPTPNTGWKTNKYGTLYKSESASFTPNTDIITRTTGPFRSMPQSGVLKAGQTIH
-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200

50-------460-------470-------480-------490---
YDEVMKQDGHVWVGYTGNSGQRIYLPVRTWNKSTNTLGVLWGTIK
|||||||||||||||||||||||||||||||||||||||||||||
YDEVMKQDGHVWVGYTGNSGQRIYLPVRTWNKSTNTLGVLWGTIK
-------210-------220-------230-------240-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	245	0	0	100.0

Content subtype: combined_34121_5nmy.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	3		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	2392		97.1 (chain: A, length: 245)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	5716 (1)	noe	95.5 (chain: A, length: 245)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	6 (1)	undefined	100.0 (chain: B, length: 1)
3	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	88 (1)	hbond	11.4 (chain: A, length: 245)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_5	OK	277 (277)	.	80.4 (chain: A, length: 245)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 245, Sequence coverage: 97.1%
- Total number of assignments
  - ¹H chemical shifts: 1384
  - ¹³C chemical shifts: 763
  - ¹⁵N chemical shifts: 245
- 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)
279	HIS	HD1	11.611
279	HIS	ND1	168.374
362	HIS	HE2	12.794
362	HIS	NE2	163.37
458	HIS	HD1	11.94
458	HIS	ND1	167.207

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1451	1381	95.2
¹³C chemical shifts	1092	763	69.9
¹⁵N chemical shifts	273	242	88.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	514	476	92.6
¹³C chemical shifts	490	235	48.0
¹⁵N chemical shifts	233	207	88.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	937	905	96.6
¹³C chemical shifts	602	528	87.7
¹⁵N chemical shifts	40	35	87.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	116	115	99.1
¹³C chemical shifts	116	114	98.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	165	159	96.4
¹³C chemical shifts	157	97	61.8
¹⁵N chemical shifts	8	8	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 245, Sequence coverage: 95.5%
- Total number of restraints: 5711
- Weight of restraints: 1.0 (5711)
- Potential type of restraints: upper-bound-parabolic (5711)
- Range of distance target values: 2.4, 5.94 (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
- Saveframe: DYANA/DIANA_distance_constraints_3
  - Status: OK
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: B, Chain length: 1, Sequence coverage: 100.0%
  - Total number of restraints: 6
  - Weight of restraints: 1.0 (6)
  - Potential type of restraints: upper-bound-parabolic (6)
  - Range of distance target values: 1.9, 2.1 (Å)
  - Histogram of distance target values
  - Histogram of discrepancy in distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map
  - Saveframe: DYANA/DIANA_distance_constraints_4
    - Status: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 245, Sequence coverage: 11.4%
    - Total number of restraints: 88
    - Weight of restraints: 1.0 (88)
    - Potential type of restraints: upper-bound-parabolic (88)
    - Range of distance target values: 1.8, 3.0 (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

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 245, Sequence coverage: 80.4%
- Total number of restraints: 277
- Total number of restraints per polymer type: 277
- Weight of restraints: 1.0 (277)
- Potential type of restraints: square-well-parabolic (277)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords M23, bacterial SH3, hydrolase, peptidase, peptidoglycan

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 (0.613 seconds)

BMRB: 34121

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Lysostaphin (E.C.3.4.24.75), entity 1, : 1 : 5 entities Detail

Experiments performed 14 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

Instrument

Sample

Instrument

Sample

NMR combined restraints 6 contents Detail