BMRBj - BMREntryMaster

Found 1 Document (0.663 seconds)

BMRB: 16040

2KB6

Solution structure of onconase C87A/C104A

Authors

Weininger, U., Schulenburg, C., Arnold, U., Ulbrich-Hofmann, R., Balbach, J.

Assembly

onconase C87A/C104A

Entity

1. onconase C87A/C104A (polymer, Thiol state: all disulfide bound), 104 monomers, 11763.36 Da Detail

XDWLTFQKKH ITNTRDVDCD NIMSTNLFHC KDKNTFIYSR PEPVKAICKG IIASKNVLTT SEFYLSDCNV TSRPCKYKLK KSTNKFAVTC ENQAPVHFVG VGSA

Formula weight

11763.36 Da

Entity Connection

disulfide 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS19:SG	1:CYS68:SG
2	disulfide	sing	1:CYS30:SG	1:CYS75:SG
3	disulfide	sing	1:CYS48:SG	1:CYS90:SG

Source organism

Lithobates pipiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.0 %, Completeness: 98.2 %, Completeness (bb): 99.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹⁵N
All	98.2 % (728 of 741)	98.3 % (620 of 631)	98.2 % (108 of 110)
Backbone	99.3 % (302 of 304)	100.0 % (205 of 205)	98.0 % (97 of 99)
Sidechain	97.5 % (426 of 437)	97.4 % (415 of 426)	100.0 % (11 of 11)
Aromatic	100.0 % (55 of 55)	100.0 % (54 of 54)	100.0 % (1 of 1)
Methyl	100.0 % (53 of 53)	100.0 % (53 of 53)

1. onconase C87A/C104A

XDWLTFQKKH ITNTRDVDCD NIMSTNLFHC KDKNTFIYSR PEPVKAICKG IIASKNVLTT SEFYLSDCNV TSRPCKYKLK KSTNKFAVTC ENQAPVHFVG VGSA

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	entity	[U-15N]	1.0 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	sodium phosphate	natural abundance	50 mM

Protein Blocks Logo

Calculated from 10 models in PDB: 2KB6, Strand ID: A Detail

Release date

2009-11-01

Citation

The folding pathway of onconase is directed by a conserved intermediate
Schulenburg, C., Low, C., Weininger, U., Mrestani-Klaus, C., Hofmann, H., Balbach, J., Ulbrich-Hofmann, R., Arnold, U.
Biochemistry (2009), 48, 8449-8457, PubMed 19655705 , DOI 10.1021/bi900596j , Abstract

Related entities 1. onconase C87A/C104A, : 1 : 12 : 154 entities Detail

Experiments performed 4 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_16040_2kb6.nef
Input source #2: Coordindates	2kb6.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	True (see coodinates for details)
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:19:CYS:SG	A:68:CYS:SG	unknown	unknown	2.027
A:30:CYS:SG	A:75:CYS:SG	unknown	unknown	2.03
A:48:CYS:SG	A:90:CYS:SG	unknown	unknown	2.02

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)
1:1:PCA:C	1:2:ASP:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	1	PCA	PYROGLUTAMIC ACID	Assigned chemical shifts, Distance restraints, Coordinates

Sequence alignments

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

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

----
VGSA
||||
VGSA

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	104	0	0	100.0

Content subtype: combined_16040_2kb6.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	747		100.0 (chain: A, length: 104)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	2644 (1)	noe	100.0 (chain: A, length: 104)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	132 (132)	.	87.5 (chain: A, length: 104)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 104, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 638
  - ¹⁵N chemical shifts: 109
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
8	LYS	HZ1	7.341
8	LYS	HZ2	7.341
8	LYS	HZ3	7.341
31	LYS	HZ1	7.089
31	LYS	HZ2	7.089
31	LYS	HZ3	7.089
33	LYS	HZ1	6.935
33	LYS	HZ2	6.935
33	LYS	HZ3	6.935
78	LYS	HZ1	7.088
78	LYS	HZ2	7.088
78	LYS	HZ3	7.088

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	637	625	98.1
¹⁵N chemical shifts	114	109	95.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	207	206	99.5
¹⁵N chemical shifts	100	98	98.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	430	419	97.4
¹⁵N chemical shifts	14	11	78.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	54	53	98.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	54	54	100.0
¹⁵N chemical shifts	1	1	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 104, Sequence coverage: 100.0%
- Total number of restraints: 2644
- Weight of restraints: 1.0 (2644)
- Potential type of restraints: square-well-parabolic (2644)
- Range of distance target values: 1.72, 5.65 (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: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 104, Sequence coverage: 87.5%
- Total number of restraints: 132
- Total number of restraints per polymer type: 132
- Weight of restraints: 1.0 (132)
- Potential type of restraints: square-well-parabolic (132)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords protein, RNase

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 (0.663 seconds)

BMRB: 16040

Sample

Related entities 1. onconase C87A/C104A, : 1 : 12 : 154 entities Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail