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BMRB: 25969

2NBA

Solution NMR structure of the DNA-binding type IV pilin ComP from Neisseri subflava

Authors

Berry, J.L., Xu, Y.

Assembly

minor DNA-uptake pilin ComP

Entity

1. minor DNA-uptake pilin ComP (polymer), 119 monomers, 13048.91 Da Detail

HRSANLRAAH AALLENARFM EQFYAKKGSF KLTSTKWPEL PVKEAGGFCI RMSGQAKGIL EGKFTLKAVA LDREAEPRVL RLNESLTAVV CGKMKGKGSC TDGEEIFRGN DAECRPFTG

Formula weight

13048.91 Da

Source organism

Neisseria subflava

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 95.3 %, Completeness (bb): 99.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	95.3 % (1303 of 1367)	94.3 % (675 of 716)	97.0 % (513 of 529)	94.3 % (115 of 122)
Backbone	99.2 % (700 of 706)	98.4 % (242 of 246)	99.7 % (344 of 345)	99.1 % (114 of 115)
Sidechain	92.4 % (710 of 768)	92.1 % (433 of 470)	94.8 % (276 of 291)	14.3 % (1 of 7)
Aromatic	70.4 % (69 of 98)	71.4 % (35 of 49)	68.8 % (33 of 48)	100.0 % (1 of 1)
Methyl	100.0 % (116 of 116)	100.0 % (58 of 58)	100.0 % (58 of 58)

1. entity

HRSANLRAAH AALLENARFM EQFYAKKGSF KLTSTKWPEL PVKEAGGFCI RMSGQAKGIL EGKFTLKAVA LDREAEPRVL RLNESLTAVV CGKMKGKGSC TDGEEIFRGN DAECRPFTG

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	ComP	[U-98% 13C; U-98% 15N]		750 uM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: -0.22 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.22 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.01 ppm, Outliers: 3 Detail

LACS Plot; CO

Referencing offset: -0.09 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2016-05-22

Citation

A Comparative Structure/Function Analysis of Two Type IV Pilin DNA Receptors Defines a Novel Mode of DNA Binding
Berry, J., Xu, Y., Ward, P., Lea, S., Matthews, S., Pelicic, V.
Structure (2016), 24, 926-934, PubMed 27161979 , DOI 10.1016/j.str.2016.04.001 , Abstract

Related entities 1. minor DNA-uptake pilin ComP, : 1 : 6 entities Detail

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	ComP	[U-98% 13C; U-98% 15N]		750 uM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

2 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	ComP	[U-98% 13C; U-98% 15N]		750 uM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

3 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	ComP	[U-98% 13C; U-98% 15N]		750 uM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

4 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	ComP	[U-98% 13C; U-98% 15N]		750 uM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

5 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	ComP	[U-98% 13C; U-98% 15N]		750 uM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

6 3D HBHA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	ComP	[U-98% 13C; U-98% 15N]		750 uM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

7 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	ComP	[U-98% 13C; U-98% 15N]		750 uM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

8 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	ComP	[U-98% 13C; U-98% 15N]		750 uM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

NMR combined restraints 2 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts	combined_25969_2nba.nef
Input source #2: Coordindates	2nba.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Error

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:54:CYS:SG	A:105:CYS:SG	oxidized, CA 54.997, CB 44.496 ppm	oxidized, CA 57.136, CB 40.412 ppm	2.023
A:96:CYS:SG	A:119:CYS:SG	oxidized, CA 54.269, CB 46.455 ppm	oxidized, CA 56.164, CB 44.458 ppm	2.025

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--------90-------100-----
HRSANLRAAHAALLENARFMEQFYAKKGSFKLTSTKWPELPVKEAGGFCIRMSGQAKGILEGKFTLKAVALDREAEPRVLRLNESLTAVVCGKMKGKGSC
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
HRSANLRAAHAALLENARFMEQFYAKKGSFKLTSTKWPELPVKEAGGFCIRMSGQAKGILEGKFTLKAVALDREAEPRVLRLNESLTAVVCGKMKGKGSC
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

--110-------120----
TDGEEIFRGNDAECRPFTG
|||||||||||||||||||
TDGEEIFRGNDAECRPFTG
-------110---------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	119	0	0	100.0

Content subtype: combined_25969_2nba.nef

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1305		100.0 (chain: A, length: 119)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 119, Sequence coverage: 100.0%
- Total number of assignments
  - ¹³C chemical shifts: 513
  - ¹H chemical shifts: 677
  - ¹⁵N chemical shifts: 115
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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

Covalent bonds

Saveframe: assembly
- Status: OK

Keywords DNA transformation, DNA-binding, Neisseriaceae, Type Iv pilin