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Found 1 Document (1.096 seconds)

BMRB: 15357

2KHS

the solution structure of SNase complex

Authors

Geng, Y., Shan, L., Feng, Y., Wang, J.

Assembly

SNase complex

Entity

1. SNase complex (polymer, Thiol state: not present), 156 monomers, 17646.10 Da Detail

ATSTKKLHKE PATLIKAIDG DTVKLMYKGQ PMTFRLLLVD TPETKHPKKG VEKYGPEASA FTKKMVENAK KIEVEFDKGQ RTDKYGRGLA YIYADGKMVN EALVRQGLAK VAYVYKPNNT HGSVAYVYKP NNTHEQLLRK SEAQAKKEKL NIWSED

Formula weight

17646.1 Da

Source organism

Staphylococcus aureus

Exptl. method

solution NMR

Refine. method

molecular dynamics, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.4 %, Completeness: 80.6 %, Completeness (bb): 94.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	80.6 % (1512 of 1876)	78.5 % (775 of 987)	81.4 % (592 of 727)	89.5 % (145 of 162)
Backbone	94.4 % (870 of 922)	92.4 % (291 of 315)	94.8 % (434 of 458)	97.3 % (145 of 149)
Sidechain	71.2 % (783 of 1100)	72.0 % (484 of 672)	72.0 % (299 of 415)	0.0 % (0 of 13)
Aromatic	28.5 % (37 of 130)	47.7 % (31 of 65)	9.4 % (6 of 64)	0.0 % (0 of 1)
Methyl	85.8 % (139 of 162)	92.6 % (75 of 81)	79.0 % (64 of 81)

1. SNase complex -subdomain

ATSTKKLHKE PATLIKAIDG DTVKLMYKGQ PMTFRLLLVD TPETKHPKKG VEKYGPEASA FTKKMVENAK KIEVEFDKGQ RTDKYGRGLA YIYADGKMVN EALVRQGLAK VAYVYKPNNT HGSVAYVYKP NNTHEQLLRK SEAQAKKEKL NIWSED

Show sample condition

Sample

Pressure 1 atm, Temperature 300 K, pH 5.0

#	Name	Isotope labeling	Concentration
1	entity	[U-99% 13C; U-99% 15N]	1 mM
2	deuterated acetate buffer		50 mM
3	KCl		100 mM
4	NaN3		0.01 % w/v
5	H2O		90 %
6	D2O		10 %

LACS Plot; CA

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

Referencing offset: 0.04 ppm, Outliers: 2 Detail

LACS Plot; CB

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

Referencing offset: 0.04 ppm, Outliers: 2 Detail

LACS Plot; HA

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

Referencing offset: -0.02 ppm, Outliers: 2 Detail

LACS Plot; CO

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

Referencing offset: 0.3 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2007-06-30

Citation

The native-like interactions between SNase121 and SNase(111-143) fragments induce the recovery of their native-like structures and the ability to degrade DNA
Geng, Y., Feng, Y., Xie, T., Shan, L., Wang, J.
Biochemistry (2009), 48, 8692-8703, PubMed 19658434 , DOI 10.1021/bi901099s , Abstract

Related entities 1. SNase complex, : 130 entities Detail

Experiments performed 2 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15357_2khs.nef
Input source #2: Coordindates	2khs.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--------90-------100
ATSTKKLHKEPATLIKAIDGDTVKLMYKGQPMTFRLLLVDTPETKHPKKGVEKYGPEASAFTKKMVENAKKIEVEFDKGQRTDKYGRGLAYIYADGKMVN
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ATSTKKLHKEPATLIKAIDGDTVKLMYKGQPMTFRLLLVDTPETKHPKKGVEKYGPEASAFTKKMVENAKKIEVEFDKGQRTDKYGRGLAYIYADGKMVN

-------110-------120-
EALVRQGLAKVAYVYKPNNTH
|||||||||||||||||||||
EALVRQGLAKVAYVYKPNNTH

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

------130-------140-------150------
GSVAYVYKPNNTHEQLLRKSEAQAKKEKLNIWSED
|||||||||||||||||||||||||||||||||||
GSVAYVYKPNNTHEQLLRKSEAQAKKEKLNIWSED
--------10--------20--------30-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	121	0	0	100.0
B	B	35	0	0	100.0

Content subtype: combined_15357_2khs.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1480		96.7 (chain: A, length: 121), 94.3 (chain: B, length: 35)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	2701 (1)	noe	92.6 (chain: A, length: 121), 94.3 (chain: B, length: 35)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	112 (1)	hbond	42.1 (chain: A, length: 121), 54.3 (chain: B, length: 35)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	185 (185)	.	82.6 (chain: A, length: 121), 65.7 (chain: B, length: 35)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 121, Sequence coverage: 96.7%
  - Entity_assembly_ID: B, Chain length: 35, Sequence coverage: 94.3%
- Total number of assignments
  - ¹H chemical shifts: 759
  - ¹³C chemical shifts: 580
  - ¹⁵N chemical shifts: 141
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- 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
  - Chain_ID: B

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	761	581	76.3
¹³C chemical shifts	566	453	80.0
¹⁵N chemical shifts	126	109	86.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	245	225	91.8
¹³C chemical shifts	242	225	93.0
¹⁵N chemical shifts	115	109	94.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	516	356	69.0
¹³C chemical shifts	324	228	70.4
¹⁵N chemical shifts	11	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	69	59	85.5
¹³C chemical shifts	69	49	71.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	49	20	40.8
¹³C chemical shifts	49	4	8.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	226	178	78.8
¹³C chemical shifts	161	127	78.9
¹⁵N chemical shifts	41	32	78.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	70	65	92.9
¹³C chemical shifts	70	63	90.0
¹⁵N chemical shifts	34	32	94.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	156	113	72.4
¹³C chemical shifts	91	64	70.3
¹⁵N chemical shifts	7	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	16	13	81.2
¹³C chemical shifts	16	11	68.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	16	9	56.2
¹³C chemical shifts	15	0	0.0
¹⁵N chemical shifts	1	0	0.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 121, Sequence coverage: 92.6%
  - Entity_assembly_ID: B, Chain length: 35, Sequence coverage: 94.3%
- Total number of restraints: 2696
- Weight of restraints: 1.0 (2696)
- Potential type of restraints: square-well-parabolic (2696)
- Range of distance target values: 2.15, 4.15 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- 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: 121, Sequence coverage: 42.1%
    - Entity_assembly_ID: B, Chain length: 35, Sequence coverage: 54.3%
  - Total number of restraints: 112
  - Weight of restraints: 1.0 (112)
  - Potential type of restraints: square-well-parabolic (112)
  - Range of distance target values: 2.0, 3.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - 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: 121, Sequence coverage: 82.6%
  - Entity_assembly_ID: B, Chain length: 35, Sequence coverage: 65.7%
- Total number of restraints: 185
- Total number of restraints per polymer type: 185
- Weight of restraints: 1.0 (185)
- Potential type of restraints: square-well-parabolic (185)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

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Found 1 Document (1.096 seconds)

BMRB: 15357

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. SNase complex, : 130 entities Detail

Experiments performed 2 experiments Detail

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail