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Found 1 Document (0.616 seconds)

BMRB: 27349

6C00

1H, 13C, 15N chemical shift assignments of initiation factor 1 from Clostridium difficile

Authors

Zhang, Y., Aguilar, F.

Assembly

C. difficile IF1

Entity

1. C. difficile IF1 (polymer, Thiol state: all free), 83 monomers, 9636.109 Da Detail

MASMAKKDVI ELEGTVSEAL PNAMFKVKLE NGHEILCHIS GKLRMNFIRI LEGDKVNVEL SPYDLTRGRI TWRKKLEHHH HHH

Formula weight

9636.109 Da

Source organism

Clostridioides difficile

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 90.4 %, Completeness: 78.7 %, Completeness (bb): 88.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	78.7 % (788 of 1001)	77.1 % (404 of 524)	79.0 % (309 of 391)	87.2 % (75 of 86)
Backbone	88.9 % (439 of 494)	89.9 % (152 of 169)	87.7 % (214 of 244)	90.1 % (73 of 81)
Sidechain	71.6 % (419 of 585)	71.0 % (252 of 355)	73.3 % (165 of 225)	40.0 % (2 of 5)
Aromatic	33.3 % (24 of 72)	50.0 % (18 of 36)	14.3 % (5 of 35)	100.0 % (1 of 1)
Methyl	94.7 % (89 of 94)	93.6 % (44 of 47)	95.7 % (45 of 47)

1. C difficile IF1

MASMAKKDVI ELEGTVSEAL PNAMFKVKLE NGHEILCHIS GKLRMNFIRI LEGDKVNVEL SPYDLTRGRI TWRKKLEHHH HHH

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.1

#	Name	Isotope labeling	Type	Concentration
1	C. difficile IF1	[U-99% 15N]		1 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.1

#	Name	Isotope labeling	Type	Concentration
2	C. difficile IF1	[U-99% 13C; U-99% 15N]		1 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.1

#	Name	Isotope labeling	Type	Concentration
3	C. difficile IF1	[U-99% 13C; U-99% 15N]		1 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.08 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.08 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.1 ppm, Outliers: 3 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.56 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 15 models in PDB: 6C00, Strand ID: A Detail

Release date

2017-12-25

Citation

¹H, ¹³C and ¹⁵N resonance assignments and structure prediction of translation initiation factor 1 from Clostridium difficile
Aguilar, F., Banaei, N., Zhang, Y.
Biomol. NMR Assign. (2018), 13, 91-95, PubMed 30370502 , DOI 10.1007/s12104-018-9858-8 , Abstract

Related entities 1. C. difficile IF1, : 1 : 1 : 127 entities Detail

Experiments performed 8 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_27349_6c00.nef
Input source #2: Coordindates	6c00.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
MASMAKKDVIELEGTVSEALPNAMFKVKLENGHEILCHISGKLRMNFIRILEGDKVNVELSPYDLTRGRITWRKKLEHHHHHH
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MASMAKKDVIELEGTVSEALPNAMFKVKLENGHEILCHISGKLRMNFIRILEGDKVNVELSPYDLTRGRITWRKKLEHHHHHH
--------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	83	0	0	100.0

Content subtype: combined_27349_6c00.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	803		89.2 (chain: A, length: 83)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1152 (1)	noe	83.1 (chain: A, length: 83)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	29 (1)	hbond	43.4 (chain: A, length: 83)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	112 (112)	.	81.9 (chain: A, length: 83)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 83, Sequence coverage: 89.2%
- Total number of assignments
  - ¹H chemical shifts: 429
  - ¹³C chemical shifts: 300
  - ¹⁵N chemical shifts: 74
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	524	389	74.2
¹³C chemical shifts	391	300	76.7
¹⁵N chemical shifts	91	74	81.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	169	150	88.8
¹³C chemical shifts	166	143	86.1
¹⁵N chemical shifts	81	72	88.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	355	239	67.3
¹³C chemical shifts	225	157	69.8
¹⁵N chemical shifts	10	2	20.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	51	47	92.2
¹³C chemical shifts	51	48	94.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	36	18	50.0
¹³C chemical shifts	35	0	0.0
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 83, Sequence coverage: 83.1%
- Total number of restraints: 1151
- Weight of restraints: 1.0 (1151)
- Potential type of restraints: square-well-parabolic (1151)
- Range of distance target values: 1.15, 6.25 (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_4
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 83, Sequence coverage: 43.4%
  - Total number of restraints: 29
  - Weight of restraints: 1.0 (29)
  - Potential type of restraints: square-well-parabolic (29)
  - Range of distance target values: 1.0, 1.65 (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_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 83, Sequence coverage: 81.9%
- Total number of restraints: 112
- Total number of restraints per polymer type: 112
- Weight of restraints: 1.0 (112)
- Potential type of restraints: square-well-parabolic (112)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

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Found 1 Document (0.616 seconds)

BMRB: 27349

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. C. difficile IF1, : 1 : 1 : 127 entities Detail

Experiments performed 8 experiments Detail

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NMR combined restraints 5 contents Detail