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BMRB: 19198

2M7O

NMR Structure of the protein NP_346341.1 from Streptococcus pneumoniae

Authors

Proudfoot, A., Serrano, P., Geralt, M., Wuthrich, K.

Assembly

SP18156A

Entity

1. SP18156A (polymer, Thiol state: not present), 70 monomers, 8180.911 Da Detail

GDDRKLMKTQ EELTEIVRDH FSDMGEIATL YVQVYESSLE SLVGGVIFED GRHYTFVYEN EDLVYEEEVL

Formula weight

8180.911 Da

Source organism

Streptococcus pneumoniae

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.1 %, Completeness: 83.4 %, Completeness (bb): 77.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	83.4 % (680 of 815)	89.2 % (373 of 418)	73.1 % (237 of 324)	95.9 % (70 of 73)
Backbone	77.4 % (325 of 420)	89.0 % (129 of 145)	62.9 % (129 of 205)	95.7 % (67 of 70)
Sidechain	90.7 % (417 of 460)	89.4 % (244 of 273)	92.4 % (170 of 184)	100.0 % (3 of 3)
Aromatic	89.7 % (70 of 78)	94.9 % (37 of 39)	84.6 % (33 of 39)
Methyl	96.3 % (79 of 82)	95.1 % (39 of 41)	97.6 % (40 of 41)

1. entity

GDDRKLMKTQ EELTEIVRDH FSDMGEIATL YVQVYESSLE SLVGGVIFED GRHYTFVYEN EDLVYEEEVL

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		5 mM

LACS Plot; CA

Referencing offset: 1.92 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 1.92 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.04 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2M7O, Strand ID: A Detail

Release date

2013-05-12

Citation

NMR Structure of the protein NP_346341.1 from Streptococcus pneumoniae
Proudfoot, A., Wuthrich, K.
Not known

Related entities 1. SP18156A, : 1 : 2 entities Detail

Experiments performed 7 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		5 mM

2 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		5 mM

3 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		5 mM

4 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		5 mM

5 APSY 4D-HACANH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		5 mM

6 APSY 5D-CBCACONH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		5 mM

7 APSY 5D-HACACONH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		5 mM

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_19198_2m7o.nef
Input source #2: Coordindates	2m7o.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
GDDRKLMKTQEELTEIVRDHFSDMGEIATLYVQVYESSLESLVGGVIFEDGRHYTFVYENEDLVYEEEVL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GDDRKLMKTQEELTEIVRDHFSDMGEIATLYVQVYESSLESLVGGVIFEDGRHYTFVYENEDLVYEEEVL

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	70	0	0	100.0

Content subtype: combined_19198_2m7o.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	694		97.1 (chain: A, length: 70)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	1357 (1)	noe	97.1 (chain: A, length: 70)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 70, Sequence coverage: 97.1%
- Total number of assignments
  - ¹H chemical shifts: 391
  - ¹⁵N chemical shifts: 70
  - ¹³C chemical shifts: 233
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 70, Sequence coverage: 97.1%
- Total number of restraints: 1357
- Weight of restraints: 1.0 (1357)
- Potential type of restraints: upper-bound-parabolic (1357)
- Range of distance target values: 2.4, 5.5 (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 Structural Genomics, Unknown Function