BMRBj - BMREntryMaster

Found 1 Document (0.533 seconds)

BMRB: 15438

2JUB

Solution structure of IPI*

Authors

Rifat, D., Wright, N.T., Varney, K.M., Weber, D.J., Black, L.W.

Assembly

IP1*

Entity

1. IP1* (polymer, Thiol state: all free), 76 monomers, 8045.265 Da Detail

ATLTSEVIKA NKGREGKPMI SLVDGEEIKG TVYLGDGWSA KKDGATIVIS PAEETALFKA KHISAAHLKI IAKNLL

Formula weight

8045.265 Da

Source organism

Escherichia virus T4

Exptl. method

Refine. method

distance geometry simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.4 %, Completeness: 78.6 %, Completeness (bb): 84.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	78.6 % (678 of 863)	82.5 % (367 of 445)	70.1 % (239 of 341)	93.5 % (72 of 77)
Backbone	84.3 % (381 of 452)	96.2 % (151 of 157)	71.5 % (158 of 221)	97.3 % (72 of 74)
Sidechain	75.8 % (364 of 480)	75.0 % (216 of 288)	78.3 % (148 of 189)	0.0 % (0 of 3)
Aromatic	0.0 % (0 of 38)	0.0 % (0 of 19)	0.0 % (0 of 18)	0.0 % (0 of 1)
Methyl	83.0 % (88 of 106)	81.1 % (43 of 53)	84.9 % (45 of 53)

1. IP1*

ATLTSEVIKA NKGREGKPMI SLVDGEEIKG TVYLGDGWSA KKDGATIVIS PAEETALFKA KHISAAHLKI IAKNLL

Show sample condition

Sample

Pressure 1 atm, Temperature 310 K, pH 4.8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		500 mM
2	sodium acetate	natural abundance		20 mM
3	D2O			10 %
4	H2O	natural abundance		90 %

LACS Plot; CA

Referencing offset: 0.3 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 0.3 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.01 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2007-08-16

Citation

Restriction endonuclease inhibitor IPI* of bacteriophage T4: a novel structure for a dedicated target
Rifat, D., Wright, N.T., Varney, K.M., Weber, D.J., Black, L.W.
J. Mol. Biol. (2008), 375, 720-734, PubMed 18037438 , DOI 10.1016/j.jmb.2007.10.064 , Abstract

Related entities 1. IP1*, : 1 : 1 : 5 entities Detail

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz with cryoprobe

Sample

State isotropic, Pressure 1 atm, Temperature 310 K, pH 4.8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		500 mM
2	sodium acetate	natural abundance		20 mM
3	D2O			10 %
4	H2O	natural abundance		90 %

2 3D HNCO

Instrument

Bruker DMX - 600 MHz with cryoprobe

Sample

State isotropic, Pressure 1 atm, Temperature 310 K, pH 4.8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		500 mM
2	sodium acetate	natural abundance		20 mM
3	D2O			10 %
4	H2O	natural abundance		90 %

3 3D HNCACB

Instrument

Bruker DMX - 600 MHz with cryoprobe

Sample

State isotropic, Pressure 1 atm, Temperature 310 K, pH 4.8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		500 mM
2	sodium acetate	natural abundance		20 mM
3	D2O			10 %
4	H2O	natural abundance		90 %

4 3D CBCA(CO)NH

Instrument

Bruker DMX - 600 MHz with cryoprobe

Sample

State isotropic, Pressure 1 atm, Temperature 310 K, pH 4.8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		500 mM
2	sodium acetate	natural abundance		20 mM
3	D2O			10 %
4	H2O	natural abundance		90 %

5 3D H(CCO)NH

Instrument

Bruker DMX - 600 MHz with cryoprobe

Sample

State isotropic, Pressure 1 atm, Temperature 310 K, pH 4.8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		500 mM
2	sodium acetate	natural abundance		20 mM
3	D2O			10 %
4	H2O	natural abundance		90 %

6 3D C(CO)NH

Instrument

Bruker DMX - 600 MHz with cryoprobe

Sample

State isotropic, Pressure 1 atm, Temperature 310 K, pH 4.8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		500 mM
2	sodium acetate	natural abundance		20 mM
3	D2O			10 %
4	H2O	natural abundance		90 %

7 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz with cryoprobe

Sample

State isotropic, Pressure 1 atm, Temperature 310 K, pH 4.8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		500 mM
2	sodium acetate	natural abundance		20 mM
3	D2O			10 %
4	H2O	natural abundance		90 %

8 4D 15N-13C NOESY

Instrument

Bruker Avance - 800 MHz with cryoprobe

Sample

State isotropic, Pressure 1 atm, Temperature 310 K, pH 4.8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		500 mM
2	sodium acetate	natural abundance		20 mM
3	D2O			10 %
4	H2O	natural abundance		90 %

9 4D 13C-13C NOESY

Instrument

Bruker Avance - 800 MHz with cryoprobe

Sample

State isotropic, Pressure 1 atm, Temperature 310 K, pH 4.8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		500 mM
2	sodium acetate	natural abundance		20 mM
3	D2O			10 %
4	H2O	natural abundance		90 %

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_15438_2jub.nef
Input source #2: Coordindates	2jub.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

None

Sequence alignments

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

--------10--------20--------30--------40--------50--------60--------70------
ATLTSEVIKANKGREGKPMISLVDGEEIKGTVYLGDGWSAKKDGATIVISPAEETALFKAKHISAAHLKIIAKNLL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ATLTSEVIKANKGREGKPMISLVDGEEIKGTVYLGDGWSAKKDGATIVISPAEETALFKAKHISAAHLKIIAKNLL

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	76	0	0	100.0

Content subtype: combined_15438_2jub.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Error	668		100.0 (chain: A, length: 76)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1639 (1)	noe	100.0 (chain: A, length: 76)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	38 (1)	hbond	35.5 (chain: A, length: 76)
3	Distance restraints	CNS/XPLOR_distance_constraints_5	Warning	8 (1)	hbond	5.3 (chain: A, length: 76)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_6	OK	85 (85)	.	78.9 (chain: A, length: 76)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_7	OK	39 (39)	.	51.3 (chain: A, length: 76)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Error
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 76, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 375
  - ¹³C chemical shifts: 217
  - ¹⁵N chemical shifts: 76
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 76, Sequence coverage: 100.0%
- Total number of restraints: 1622
- Weight of restraints: 1.0 (1622)
- Potential type of restraints: square-well-parabolic (1622)
- Range of distance target values: 2.35, 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
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 76, Sequence coverage: 35.5%
  - Total number of restraints: 38
  - Weight of restraints: 1.0 (38)
  - Potential type of restraints: square-well-parabolic (38)
  - Range of distance target values: 2.6, 2.95 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_5
    - Status: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 76, Sequence coverage: 5.3%
    - Total number of restraints: 8
    - Weight of restraints: 1.0 (8)
    - Potential type of restraints: square-well-parabolic (8)
    - Range of distance target values: 2.6, 2.95 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_6
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 76, Sequence coverage: 78.9%
- Total number of restraints: 85
- Total number of restraints per polymer type: 85
- Weight of restraints: 1.0 (85)
- Potential type of restraints: square-well-parabolic (85)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_7
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 76, Sequence coverage: 51.3%
- Total number of restraints: 39
- Potential type of restraints: undefined (39)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue
  - Chain_ID: A
    None