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BMRB: 18484

2LTJ

Conformational analysis of StrH, the surface-attached exo- -D-N-acetylglucosaminidase from Streptococcus pneumoniae.

Authors

Pluvinage, B., Chitayat, S., Ficko-Blean, E., Abbott, D., Kunjachen, J., Grondin, J., Spencer, H., Smith, S., Boraston, A.

Assembly

G5

Entity

1. G5 (polymer, Thiol state: all free), 111 monomers, 12137.34 Da Detail

MGSSHHHHHS SGLVPRGSHM SLDENEVAAN VETRPELITR TEEIPFEVIK KENPNLPAGQ ENIITAGVKG ERTHYISVLT ENGKTTETVL DSQVTKEVIN QVVEVGAPVT H

Formula weight

12137.34 Da

Source organism

Streptococcus pneumoniae

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 91.9 %, Completeness: 79.0 %, Completeness (bb): 74.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	79.0 % (974 of 1233)	87.7 % (558 of 636)	64.9 % (313 of 482)	89.6 % (103 of 115)
Backbone	74.2 % (485 of 654)	89.3 % (200 of 224)	58.5 % (190 of 325)	90.5 % (95 of 105)
Sidechain	84.9 % (579 of 682)	86.9 % (358 of 412)	81.9 % (213 of 260)	80.0 % (8 of 10)
Aromatic	16.0 % (8 of 50)	32.0 % (8 of 25)	0.0 % (0 of 25)
Methyl	97.1 % (132 of 136)	97.1 % (66 of 68)	97.1 % (66 of 68)

1. entity

MGSSHHHHHS SGLVPRGSHM SLDENEVAAN VETRPELITR TEEIPFEVIK KENPNLPAGQ ENIITAGVKG ERTHYISVLT ENGKTTETVL DSQVTKEVIN QVVEVGAPVT H

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	G5	[U-100% 13C; U-100% 15N]		1 mM
2	TRIS	natural abundance		25 mM
3	sodium chloride	natural abundance		25 mM
4	DSS	natural abundance		0.5 mM
5	DTT	natural abundance		1 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: 0.2 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: 0.2 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: -0.01 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 21 models in PDB: 2LTJ, Strand ID: A Detail

Release date

2012-11-26

Citation

Conformational analysis of StrH, the surface-attached exo-β-D-N-acetylglucosaminidase from Streptococcus pneumoniae
Pluvinage, B., Chitayat, S., Ficko-Blean, E., Abbott, D., Kunjachen, J., Grondin, J., Spencer, H.L., Smith, S.P., Boraston, A.B.
J. Mol. Biol. (2013), 425, 334-349, PubMed 23154168 , DOI 10.1016/j.jmb.2012.11.005 , Abstract

Related entities 1. G5, : 1 : 7 entities Detail

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	G5	[U-100% 13C; U-100% 15N]		1 mM
2	TRIS	natural abundance		25 mM
3	sodium chloride	natural abundance		25 mM
4	DSS	natural abundance		0.5 mM
5	DTT	natural abundance		1 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

2 3D CBCA(CO)NH

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	G5	[U-100% 13C; U-100% 15N]		1 mM
2	TRIS	natural abundance		25 mM
3	sodium chloride	natural abundance		25 mM
4	DSS	natural abundance		0.5 mM
5	DTT	natural abundance		1 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

3 2D 1H-1H NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	G5	[U-100% 13C; U-100% 15N]		1 mM
2	TRIS	natural abundance		25 mM
3	sodium chloride	natural abundance		25 mM
4	DSS	natural abundance		0.5 mM
5	DTT	natural abundance		1 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

4 2D 1H-1H TOCSY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	G5	[U-100% 13C; U-100% 15N]		1 mM
2	TRIS	natural abundance		25 mM
3	sodium chloride	natural abundance		25 mM
4	DSS	natural abundance		0.5 mM
5	DTT	natural abundance		1 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

5 3D C(CO)NH

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	G5	[U-100% 13C; U-100% 15N]		1 mM
2	TRIS	natural abundance		25 mM
3	sodium chloride	natural abundance		25 mM
4	DSS	natural abundance		0.5 mM
5	DTT	natural abundance		1 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

6 3D HNCACB

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	G5	[U-100% 13C; U-100% 15N]		1 mM
2	TRIS	natural abundance		25 mM
3	sodium chloride	natural abundance		25 mM
4	DSS	natural abundance		0.5 mM
5	DTT	natural abundance		1 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

7 3D CBCA(CO)NH

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	G5	[U-100% 13C; U-100% 15N]		1 mM
2	TRIS	natural abundance		25 mM
3	sodium chloride	natural abundance		25 mM
4	DSS	natural abundance		0.5 mM
5	DTT	natural abundance		1 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

8 3D H(CCO)NH

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	G5	[U-100% 13C; U-100% 15N]		1 mM
2	TRIS	natural abundance		25 mM
3	sodium chloride	natural abundance		25 mM
4	DSS	natural abundance		0.5 mM
5	DTT	natural abundance		1 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

9 3D HCCH-TOCSY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	G5	[U-100% 13C; U-100% 15N]		1 mM
2	TRIS	natural abundance		25 mM
3	sodium chloride	natural abundance		25 mM
4	DSS	natural abundance		0.5 mM
5	DTT	natural abundance		1 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

10 3D 1H-15N NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	G5	[U-100% 13C; U-100% 15N]		1 mM
2	TRIS	natural abundance		25 mM
3	sodium chloride	natural abundance		25 mM
4	DSS	natural abundance		0.5 mM
5	DTT	natural abundance		1 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

11 3D 1H-13C NOESY aliphatic

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	G5	[U-100% 13C; U-100% 15N]		1 mM
2	TRIS	natural abundance		25 mM
3	sodium chloride	natural abundance		25 mM
4	DSS	natural abundance		0.5 mM
5	DTT	natural abundance		1 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_18484_2ltj.nef
Input source #2: Coordindates	2ltj.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	Error

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	3	.	Not matched with CCD	None
A	4	.	Not matched with CCD	None
A	5	.	Not matched with CCD	None
A	6	.	Not matched with CCD	None
A	7	.	Not matched with CCD	None
A	8	.	Not matched with CCD	None
A	9	.	Not matched with CCD	None
A	15	.	Not matched with CCD	None
A	17	.	Not matched with CCD	None
A	18	.	Not matched with CCD	None
A	19	.	Not matched with CCD	None

Sequence alignments

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

---------10---- -- - - 20--------30--------40--------50--------60--------70--------80--------90-----
..G.......SSGLV-R.-.-S-DENEVAANVETRPELITRTEEIPFEVIKKENPNLPAGQENIITAGVKGERTHYISVLTENGKTTETVLDSQVTKEVI
          ||||| |   ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGSSHHHHHHSSGLVPRGSHMSLDENEVAANVETRPELITRTEEIPFEVIKKENPNLPAGQENIITAGVKGERTHYISVLTENGKTTETVLDSQVTKEVI
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

--100-------
NQVVEVGAPVTH
||||||||||||
NQVVEVGAPVTH
-------110--

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	112	12	1	88.4

Content subtype: combined_18484_2ltj.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	955		90.0 (chain: A, length: 110)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	2402 (1)	noe	68.2 (chain: A, length: 110)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 110, Sequence coverage: 90.0%
- Total number of assignments
  - ¹H chemical shifts: 545
  - ¹⁵N chemical shifts: 101
  - ¹³C chemical shifts: 309
- 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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 110, Sequence coverage: 68.2%
- Total number of restraints: 2259
- Weight of restraints: 1.0 (2259)
- Potential type of restraints: square-well-parabolic (2259)
- Range of distance target values: 2.4, 3.9 (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 b-sheet, elongated