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BMRB: 19155

2M6U

NMR Structure of CbpAN from Streptococcus pneumoniae

Authors

Liu, A., Yan, H., Achila, D., Martinez-Hackert, E., Li, Y., Banerjee, R.

Assembly

CbpAN from Streptococcus pneumoniae

Entity

1. CbpAN from Streptococcus pneumoniae (polymer), 85 monomers, 9831.088 Da Detail

GHMLDSERDK ARKEVEEYVK KIVGESYAKS TKKRHTITVA LVNELNNIKN EYLNKIVEST SESQLQILMM ESRSKVDEAV SKFEK

Formula weight

9831.088 Da

Source organism

Streptococcus pneumoniae

Exptl. method

Refine. method

torsion angle dynamics, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.6 %, Completeness: 92.4 %, Completeness (bb): 93.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	92.4 % (944 of 1022)	93.9 % (506 of 539)	90.3 % (353 of 391)	92.4 % (85 of 92)
Backbone	93.7 % (478 of 510)	93.0 % (160 of 172)	94.9 % (240 of 253)	91.8 % (78 of 85)
Sidechain	91.8 % (546 of 595)	94.3 % (346 of 367)	87.3 % (193 of 221)	100.0 % (7 of 7)
Aromatic	54.8 % (23 of 42)	90.5 % (19 of 21)	19.0 % (4 of 21)
Methyl	94.6 % (87 of 92)	95.7 % (44 of 46)	93.5 % (43 of 46)

1. entity

GHMLDSERDK ARKEVEEYVK KIVGESYAKS TKKRHTITVA LVNELNNIKN EYLNKIVEST SESQLQILMM ESRSKVDEAV SKFEK

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 1 mM 15N/13C-labeled protein in 50 mM phosphate buffer, pH 7.0, and 50 mM NaCl

#	Name	Isotope labeling	Type	Concentration
1	DSS	natural abundance		50 uM
2	sodium azide	natural abundance		100 uM
3	sodium phosphate	natural abundance		50 mM
4	sodium chloride	natural abundance		50 mM
5	H20	natural abundance		95 %
6	D20	natural abundance		5 %
7	CbpAN_protein	15N/13C-labeled		1 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 1 mM 15N/13C-labeled CbpAN protein

#	Name	Isotope labeling	Type	Concentration
8	DSS	natural abundance		50 uM
9	sodium azide	natural abundance		100 uM
10	sodium phosphate	natural abundance		50 mM
11	sodium chloride	natural abundance		50 mM
12	D20	natural abundance		100 %
13	CbpAN_protein	15N/13C-labeled		1 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 2M6U, Strand ID: A Detail

Release date

2014-04-13

Citation

Host Specification of Factor H Binding by Streptococcus pneumoniae
Liu, A., Achila, D., Banerjee, R., Martinez-Hackert, E., Li, Y., Yan, H.
Nature

Related entities 1. CbpAN from Streptococcus pneumoniae, : 1 : 3 entities Detail

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 1 mM 15N/13C-labeled protein in 50 mM phosphate buffer, pH 7.0, and 50 mM NaCl

#	Name	Isotope labeling	Type	Concentration
1	DSS	natural abundance		50 uM
2	sodium azide	natural abundance		100 uM
3	sodium phosphate	natural abundance		50 mM
4	sodium chloride	natural abundance		50 mM
5	H20	natural abundance		95 %
6	D20	natural abundance		5 %
7	CbpAN_protein	15N/13C-labeled		1 mM

2 3D HNCA

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 1 mM 15N/13C-labeled protein in 50 mM phosphate buffer, pH 7.0, and 50 mM NaCl

#	Name	Isotope labeling	Type	Concentration
1	DSS	natural abundance		50 uM
2	sodium azide	natural abundance		100 uM
3	sodium phosphate	natural abundance		50 mM
4	sodium chloride	natural abundance		50 mM
5	H20	natural abundance		95 %
6	D20	natural abundance		5 %
7	CbpAN_protein	15N/13C-labeled		1 mM

3 3D HN(CO)CA

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 1 mM 15N/13C-labeled protein in 50 mM phosphate buffer, pH 7.0, and 50 mM NaCl

#	Name	Isotope labeling	Type	Concentration
1	DSS	natural abundance		50 uM
2	sodium azide	natural abundance		100 uM
3	sodium phosphate	natural abundance		50 mM
4	sodium chloride	natural abundance		50 mM
5	H20	natural abundance		95 %
6	D20	natural abundance		5 %
7	CbpAN_protein	15N/13C-labeled		1 mM

4 3D HNCACB

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 1 mM 15N/13C-labeled protein in 50 mM phosphate buffer, pH 7.0, and 50 mM NaCl

#	Name	Isotope labeling	Type	Concentration
1	DSS	natural abundance		50 uM
2	sodium azide	natural abundance		100 uM
3	sodium phosphate	natural abundance		50 mM
4	sodium chloride	natural abundance		50 mM
5	H20	natural abundance		95 %
6	D20	natural abundance		5 %
7	CbpAN_protein	15N/13C-labeled		1 mM

5 3D CBCA(CO)NH

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 1 mM 15N/13C-labeled protein in 50 mM phosphate buffer, pH 7.0, and 50 mM NaCl

#	Name	Isotope labeling	Type	Concentration
1	DSS	natural abundance		50 uM
2	sodium azide	natural abundance		100 uM
3	sodium phosphate	natural abundance		50 mM
4	sodium chloride	natural abundance		50 mM
5	H20	natural abundance		95 %
6	D20	natural abundance		5 %
7	CbpAN_protein	15N/13C-labeled		1 mM

6 3D HNCO

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 1 mM 15N/13C-labeled protein in 50 mM phosphate buffer, pH 7.0, and 50 mM NaCl

#	Name	Isotope labeling	Type	Concentration
1	DSS	natural abundance		50 uM
2	sodium azide	natural abundance		100 uM
3	sodium phosphate	natural abundance		50 mM
4	sodium chloride	natural abundance		50 mM
5	H20	natural abundance		95 %
6	D20	natural abundance		5 %
7	CbpAN_protein	15N/13C-labeled		1 mM

7 3D HN(CA)CO

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 1 mM 15N/13C-labeled protein in 50 mM phosphate buffer, pH 7.0, and 50 mM NaCl

#	Name	Isotope labeling	Type	Concentration
1	DSS	natural abundance		50 uM
2	sodium azide	natural abundance		100 uM
3	sodium phosphate	natural abundance		50 mM
4	sodium chloride	natural abundance		50 mM
5	H20	natural abundance		95 %
6	D20	natural abundance		5 %
7	CbpAN_protein	15N/13C-labeled		1 mM

8 3D 1H-15N NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 1 mM 15N/13C-labeled protein in 50 mM phosphate buffer, pH 7.0, and 50 mM NaCl

#	Name	Isotope labeling	Type	Concentration
1	DSS	natural abundance		50 uM
2	sodium azide	natural abundance		100 uM
3	sodium phosphate	natural abundance		50 mM
4	sodium chloride	natural abundance		50 mM
5	H20	natural abundance		95 %
6	D20	natural abundance		5 %
7	CbpAN_protein	15N/13C-labeled		1 mM

9 2D 1H-13C HSQC

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 1 mM 15N/13C-labeled CbpAN protein

#	Name	Isotope labeling	Type	Concentration
8	DSS	natural abundance		50 uM
9	sodium azide	natural abundance		100 uM
10	sodium phosphate	natural abundance		50 mM
11	sodium chloride	natural abundance		50 mM
12	D20	natural abundance		100 %
13	CbpAN_protein	15N/13C-labeled		1 mM

10 3D HCCH-TOCSY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 1 mM 15N/13C-labeled CbpAN protein

#	Name	Isotope labeling	Type	Concentration
8	DSS	natural abundance		50 uM
9	sodium azide	natural abundance		100 uM
10	sodium phosphate	natural abundance		50 mM
11	sodium chloride	natural abundance		50 mM
12	D20	natural abundance		100 %
13	CbpAN_protein	15N/13C-labeled		1 mM

11 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 1 mM 15N/13C-labeled CbpAN protein

#	Name	Isotope labeling	Type	Concentration
8	DSS	natural abundance		50 uM
9	sodium azide	natural abundance		100 uM
10	sodium phosphate	natural abundance		50 mM
11	sodium chloride	natural abundance		50 mM
12	D20	natural abundance		100 %
13	CbpAN_protein	15N/13C-labeled		1 mM

12 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 1 mM 15N/13C-labeled CbpAN protein

#	Name	Isotope labeling	Type	Concentration
8	DSS	natural abundance		50 uM
9	sodium azide	natural abundance		100 uM
10	sodium phosphate	natural abundance		50 mM
11	sodium chloride	natural abundance		50 mM
12	D20	natural abundance		100 %
13	CbpAN_protein	15N/13C-labeled		1 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19155_2m6u.nef
Input source #2: Coordindates	2m6u.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--------80--
GHMLDSERDKARKEVEEYVKKIVGESYAKSTKKRHTITVALVNELNNIKNEYLNKIVESTSESQLQILMMESRSKVDEAVSKFEK
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GHMLDSERDKARKEVEEYVKKIVGESYAKSTKKRHTITVALVNELNNIKNEYLNKIVESTSESQLQILMMESRSKVDEAVSKFEK
--------10--------20--------30--------40--------50--------60--------70--------80-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	85	0	0	100.0

Content subtype: combined_19155_2m6u.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	953		96.5 (chain: A, length: 85)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	2572 (1)	noe	96.5 (chain: A, length: 85)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	150 (150)	.	95.3 (chain: A, length: 85)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 85, Sequence coverage: 96.5%
- Total number of assignments
  - ¹H chemical shifts: 510
  - ¹³C chemical shifts: 356
  - ¹⁵N chemical shifts: 87
- 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: 85, Sequence coverage: 96.5%
- Total number of restraints: 2572
- Weight of restraints: 1.0 (2572)
- Potential type of restraints: upper-bound-parabolic (2572)
- Range of distance target values: 2.2, 5.97 (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

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 85, Sequence coverage: 95.3%
- Total number of restraints: 150
- Total number of restraints per polymer type: 150
- Weight of restraints: 1.0 (150)
- Potential type of restraints: square-well-parabolic (150)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords three-helix bundle