BMRBj - BMREntryMaster

Found 1 Document (0.49 seconds)

BMRB: 15392

2JO5

Tetrameric structure of KIA7F peptide

Authors

lopez de la Osa, J., Gonzalez, C., Laurents, D.V., Chakrabartty, A., Bateman, D.A.

Assembly

KIA7F peptide tetramer

Entity

1. KIA7F peptide tetramer (polymer, Thiol state: not present), 22 monomers, 1851.261 × 4 Da Detail

XAKAAAAAIK AIAAIIKAGG FX

Total weight

7405.044 Da

Max. entity weight

1851.261 Da

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 90.9 %, Completeness: 98.1 %, Completeness (bb): 97.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H
All	98.1 % (101 of 103)	98.1 % (101 of 103)
Backbone	97.6 % (41 of 42)	97.6 % (41 of 42)
Sidechain	98.4 % (60 of 61)	98.4 % (60 of 61)
Aromatic	100.0 % (5 of 5)	100.0 % (5 of 5)
Methyl	94.4 % (17 of 18)	94.4 % (17 of 18)

1. KIA7F

XAKAAAAAIK AIAAIIKAGG FX

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278.15 K, pH 5.0

#	Name	Isotope labeling	Concentration
1	sodium acetate	natural abundance	10 mM
2	sodium chloride	natural abundance	200 mM
3	DSS	natural abundance	0.005 mM
4	H2O		90 %
5	D2O		10 %

Protein Blocks Logo

Calculated from 10 models in PDB: 2JO5, Strand ID: A, B, C, D Detail

Release date

2008-03-12

Citation

Getting specificity from simplicity in putative proteins from the prebiotic earth
Lopez de la Osa, J., Bateman, D.A., Ho, S., Gonzalez, C., Chakrabartty, A., Laurents, D.V.
Proc. Natl. Acad. Sci. U. S. A. (2007), 104, 14941-14946, PubMed 17855563 , DOI 10.1073/pnas.0706876104 , Abstract

Experiments performed 3 experiments Detail

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_15392_2jo5.nef
Input source #2: Coordindates	2jo5.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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:2:ALA:N	1:1:ACE:C	unknown	unknown	n/a
2:2:ALA:N	2:1:ACE:C	unknown	unknown	n/a
3:2:ALA:N	3:1:ACE:C	unknown	unknown	n/a
4:2:ALA:N	4:1:ACE:C	unknown	unknown	n/a
1:21:PHE:C	1:22:NH2:N	unknown	unknown	n/a
2:21:PHE:C	2:22:NH2:N	unknown	unknown	n/a
3:21:PHE:C	3:22:NH2:N	unknown	unknown	n/a
4:21:PHE:C	4:22:NH2:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	1	ACE	ACETYL GROUP	Coordinates
A	22	NH2	AMINO GROUP	Coordinates
B	23	ACE	ACETYL GROUP	Coordinates
B	44	NH2	AMINO GROUP	Coordinates
C	45	ACE	ACETYL GROUP	Coordinates
C	66	NH2	AMINO GROUP	Coordinates
D	67	ACE	ACETYL GROUP	Coordinates
D	88	NH2	AMINO GROUP	Coordinates

Sequence alignments

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

--------10--------20--
XAKAAAAAIKAIAAIIKAGGFX
||||||||||||||||||||||
XAKAAAAAIKAIAAIIKAGGFX

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

------30--------40----
XAKAAAAAIKAIAAIIKAGGFX
||||||||||||||||||||||
XAKAAAAAIKAIAAIIKAGGFX
--------10--------20--

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

----50--------60------
XAKAAAAAIKAIAAIIKAGGFX
||||||||||||||||||||||
XAKAAAAAIKAIAAIIKAGGFX
--------10--------20--

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

--70--------80--------
XAKAAAAAIKAIAAIIKAGGFX
||||||||||||||||||||||
XAKAAAAAIKAIAAIIKAGGFX
--------10--------20--

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Sequence coverage (%)
A	A	22	100.0
B	B	22	100.0
C	C	22	100.0
D	D	22	100.0

Content subtype: combined_15392_2jo5.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	8		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Error	107		81.8 (chain: C, length: 22)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	2044 (1)	noe	90.9 (chain: A, length: 22), 90.9 (chain: B, length: 22), 90.9 (chain: C, length: 22), 90.9 (chain: D, length: 22)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Error
- Sequence coverage of experimental data
  - Entity_assembly_ID: C, Chain length: 22, Sequence coverage: 81.8%
- Total number of assignments
  - ¹H chemical shifts: 107
- Completeness of assignments
  - Entity_assemble_ID: C
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: C

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
54	LYS	HZ1	7.67
54	LYS	HZ2	7.67
54	LYS	HZ3	7.67
61	LYS	HZ1	7.63
61	LYS	HZ2	7.63
61	LYS	HZ3	7.63

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	107	91	85.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	42	38	90.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	65	53	81.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	19	17	89.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	5	0	0.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 22, Sequence coverage: 90.9%
  - Entity_assembly_ID: B, Chain length: 22, Sequence coverage: 90.9%
  - Entity_assembly_ID: C, Chain length: 22, Sequence coverage: 90.9%
  - Entity_assembly_ID: D, Chain length: 22, Sequence coverage: 90.9%
- Total number of restraints: 2044
- Weight of restraints: 1.0 (2044)
- Potential type of restraints: upper-bound-parabolic (2044)
- Range of distance target values: 1.8, 1.8 (Å)
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
  - Chain_ID: D
- Distance restraints on contact map

Keywords oligomer, peptide, prebiotic

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.49 seconds)

BMRB: 15392

Sample

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 3 contents Detail