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Found 1 Document (0.591 seconds)

BMRB: 18713

2LY8

The budding yeast chaperone Scm3 recognizes the partially unfolded dimer of the centromere-specific Cse4/H4 histone variant

Authors

Hong, J., Feng, H., Zhou, Z., Ghirlando, R., Bai, Y.

Assembly

sC4

Entity

1. sC4 (polymer, Thiol state: not present), 121 monomers, 13697.71 Da Detail

LISKIPFARL VKEVTDEFTT KDQDLRWQSM AIMALQEASE AYLVGLLEHT NLLALHLVPR GSKRISGLIY EEVRAVLKSF LESVIRDSVT YTEHAKRKTV TSLDVVYALK RQGRTLYGFG G

Formula weight

13697.71 Da

Source organism

Saccharomyces cerevisiae

Exptl. method

solution NMR

Refine. method

DGSA-distance geometry simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.7 %, Completeness: 89.3 %, Completeness (bb): 94.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.3 % (1282 of 1436)	90.8 % (673 of 741)	86.3 % (492 of 570)	93.6 % (117 of 125)
Backbone	94.0 % (679 of 722)	93.1 % (230 of 247)	94.7 % (337 of 356)	94.1 % (112 of 119)
Sidechain	86.0 % (712 of 828)	89.7 % (443 of 494)	80.5 % (264 of 328)	83.3 % (5 of 6)
Aromatic	45.2 % (47 of 104)	78.8 % (41 of 52)	11.8 % (6 of 51)	0.0 % (0 of 1)
Methyl	93.0 % (160 of 172)	93.0 % (80 of 86)	93.0 % (80 of 86)

1. sC4

LISKIPFARL VKEVTDEFTT KDQDLRWQSM AIMALQEASE AYLVGLLEHT NLLALHLVPR GSKRISGLIY EEVRAVLKSF LESVIRDSVT YTEHAKRKTV TSLDVVYALK RQGRTLYGFG G

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308.1 (±0.2) K, pH 5.4 (±0.1), Details 15N, 13C/15N or 13C/15N/D labeled single chain Cse4-H4(sC4) in 50 mM MES, pH 5.4, 308.1K.

#	Name	Isotope labeling	Concentration
1	sC4	[U-100% 15N]	0.8 (±0.05) mM
2	sC4	[U-100% 13C; U-100% 15N]	0.8 (±0.05) mM
3	sC4	[U-13C; U-15N; U-2H]	0.8 (±0.05) mM
4	sC4	[U-13C; U-15N; U-2H]	0.8 (±0.05) mM
5	H2O	natural abundance	90 (±0.05) %
6	D2O	natural abundance	10 (±0.05) %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 308.1 (±0.2) K, pH 5.4 (±0.1), Details 13C/15N labeled single chain Cse4-H4(sC4) in 50 mM MES, pH 5.4, 308.1K.

#	Name	Isotope labeling	Type	Concentration
7	sC4	[U-100% 13C; U-100% 15N]		0.8 (±0.05) mM
8	D2O	natural abundance		100 (±0.05) %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 308.1 (±0.2) K, pH 5.4 (±0.1), Details single chain Cse4-H4(sC4) in 50 mM MES, pH 5.4, 308.1K.

#	Name	Isotope labeling	Type	Concentration
9	sC4	natural abundance		0.8 (±0.05) mM
10	D2O	natural abundance		100 (±0.05) %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	sC4	Carbon	external	indirect	1.0
¹H	sC4	protons	external	direct	1.0
¹⁵N	sC4	nitrogen	external	indirect	1.0

Referencing offset: -0.11 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	sC4	Carbon	external	indirect	1.0
¹H	sC4	protons	external	direct	1.0
¹⁵N	sC4	nitrogen	external	indirect	1.0

Referencing offset: -0.11 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	sC4	Carbon	external	indirect	1.0
¹H	sC4	protons	external	direct	1.0
¹⁵N	sC4	nitrogen	external	indirect	1.0

Referencing offset: -0.02 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	sC4	Carbon	external	indirect	1.0
¹H	sC4	protons	external	direct	1.0
¹⁵N	sC4	nitrogen	external	indirect	1.0

Referencing offset: 0.31 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2LY8, Strand ID: A Detail

Release date

2012-09-19

Citation

The budding yeast chaperone Scm3 recognizes the partially unfolded dimer of the
Hong, J., Feng, H., Zhou, Z., Ghirlando, R., Bai, Y.
J. Mol. Biol.

Related entities 1. sC4, : 1 entities Detail

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308.1 (±0.2) K, pH 5.4 (±0.1), Details 15N, 13C/15N or 13C/15N/D labeled single chain Cse4-H4(sC4) in 50 mM MES, pH 5.4, 308.1K.

#	Name	Isotope labeling	Concentration
1	sC4	[U-100% 15N]	0.8 (±0.05) mM
2	sC4	[U-100% 13C; U-100% 15N]	0.8 (±0.05) mM
3	sC4	[U-13C; U-15N; U-2H]	0.8 (±0.05) mM
4	sC4	[U-13C; U-15N; U-2H]	0.8 (±0.05) mM
5	H2O	natural abundance	90 (±0.05) %
6	D2O	natural abundance	10 (±0.05) %

2 2D 1H-1H NOESY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308.1 (±0.2) K, pH 5.4 (±0.1), Details single chain Cse4-H4(sC4) in 50 mM MES, pH 5.4, 308.1K.

#	Name	Isotope labeling	Type	Concentration
9	sC4	natural abundance		0.8 (±0.05) mM
10	D2O	natural abundance		100 (±0.05) %

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	sC4	[U-100% 15N]	0.8 (±0.05) mM
2	sC4	[U-100% 13C; U-100% 15N]	0.8 (±0.05) mM
3	sC4	[U-13C; U-15N; U-2H]	0.8 (±0.05) mM
4	sC4	[U-13C; U-15N; U-2H]	0.8 (±0.05) mM
5	H2O	natural abundance	90 (±0.05) %
6	D2O	natural abundance	10 (±0.05) %

4 3D HNCACB

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	sC4	[U-100% 15N]	0.8 (±0.05) mM
2	sC4	[U-100% 13C; U-100% 15N]	0.8 (±0.05) mM
3	sC4	[U-13C; U-15N; U-2H]	0.8 (±0.05) mM
4	sC4	[U-13C; U-15N; U-2H]	0.8 (±0.05) mM
5	H2O	natural abundance	90 (±0.05) %
6	D2O	natural abundance	10 (±0.05) %

5 3D HNCO

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	sC4	[U-100% 15N]	0.8 (±0.05) mM
2	sC4	[U-100% 13C; U-100% 15N]	0.8 (±0.05) mM
3	sC4	[U-13C; U-15N; U-2H]	0.8 (±0.05) mM
4	sC4	[U-13C; U-15N; U-2H]	0.8 (±0.05) mM
5	H2O	natural abundance	90 (±0.05) %
6	D2O	natural abundance	10 (±0.05) %

6 3D HNCA

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	sC4	[U-100% 15N]	0.8 (±0.05) mM
2	sC4	[U-100% 13C; U-100% 15N]	0.8 (±0.05) mM
3	sC4	[U-13C; U-15N; U-2H]	0.8 (±0.05) mM
4	sC4	[U-13C; U-15N; U-2H]	0.8 (±0.05) mM
5	H2O	natural abundance	90 (±0.05) %
6	D2O	natural abundance	10 (±0.05) %

7 3D HN(CO)CA

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	sC4	[U-100% 15N]	0.8 (±0.05) mM
2	sC4	[U-100% 13C; U-100% 15N]	0.8 (±0.05) mM
3	sC4	[U-13C; U-15N; U-2H]	0.8 (±0.05) mM
4	sC4	[U-13C; U-15N; U-2H]	0.8 (±0.05) mM
5	H2O	natural abundance	90 (±0.05) %
6	D2O	natural abundance	10 (±0.05) %

8 3D HBHA(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308.1 (±0.2) K, pH 5.4 (±0.1), Details 13C/15N labeled single chain Cse4-H4(sC4) in 50 mM MES, pH 5.4, 308.1K.

#	Name	Isotope labeling	Type	Concentration
7	sC4	[U-100% 13C; U-100% 15N]		0.8 (±0.05) mM
8	D2O	natural abundance		100 (±0.05) %

9 3D HCCH-TOCSY

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
7	sC4	[U-100% 13C; U-100% 15N]		0.8 (±0.05) mM
8	D2O	natural abundance		100 (±0.05) %

10 3D 1H-15N NOESY

Instrument

Bruker Avance - 900 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
7	sC4	[U-100% 13C; U-100% 15N]		0.8 (±0.05) mM
8	D2O	natural abundance		100 (±0.05) %

11 3D 1H-13C NOESY

Instrument

Bruker Avance - 900 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
7	sC4	[U-100% 13C; U-100% 15N]		0.8 (±0.05) mM
8	D2O	natural abundance		100 (±0.05) %

12 2D 1H-1H NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308.1 (±0.2) K, pH 5.4 (±0.1), Details single chain Cse4-H4(sC4) in 50 mM MES, pH 5.4, 308.1K.

#	Name	Isotope labeling	Type	Concentration
9	sC4	natural abundance		0.8 (±0.05) mM
10	D2O	natural abundance		100 (±0.05) %

13 3D H(CCO)NH

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
7	sC4	[U-100% 13C; U-100% 15N]		0.8 (±0.05) mM
8	D2O	natural abundance		100 (±0.05) %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18713_2ly8.nef
Input source #2: Coordindates	2ly8.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
LISKIPFARLVKEVTDEFTTKDQDLRWQSMAIMALQEASEAYLVGLLEHTNLLALHLVPRGSKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTV
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LISKIPFARLVKEVTDEFTTKDQDLRWQSMAIMALQEASEAYLVGLLEHTNLLALHLVPRGSKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTV

-------110-------120-
TSLDVVYALKRQGRTLYGFGG
|||||||||||||||||||||
TSLDVVYALKRQGRTLYGFGG

Chain assignments

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

Content subtype: combined_18713_2ly8.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1286		96.7 (chain: A, length: 121)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	3424 (1)	noe	99.2 (chain: A, length: 121)
2	Distance restraints	CNS/XPLOR_distance_constraints_5	Warning	121 (1)	noe	28.1 (chain: A, length: 121)
3	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	118 (1)	hbond	62.0 (chain: A, length: 121)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	190 (190)	.	87.6 (chain: A, length: 121)

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%
- Total number of assignments
  - ¹H chemical shifts: 683
  - ¹³C chemical shifts: 487
  - ¹⁵N chemical shifts: 116
- Completeness of assignments
  - Entity_assemble_ID: A
- 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	741	683	92.2
¹³C chemical shifts	570	487	85.4
¹⁵N chemical shifts	134	116	86.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	247	235	95.1
¹³C chemical shifts	242	228	94.2
¹⁵N chemical shifts	119	111	93.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	494	448	90.7
¹³C chemical shifts	328	259	79.0
¹⁵N chemical shifts	15	5	33.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	88	80	90.9
¹³C chemical shifts	88	80	90.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	52	41	78.8
¹³C chemical shifts	51	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: 99.2%
- Total number of restraints: 3404
- Weight of restraints: 1.0 (3404)
- Potential type of restraints: square-well-parabolic (3404)
- Range of distance target values: 2.2, 5.25 (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_5
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 121, Sequence coverage: 28.1%
  - Total number of restraints: 118
  - Weight of restraints: 1.0 (118)
  - Potential type of restraints: square-well-parabolic (118)
  - Range of distance target values: 2.4, 4.65 (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
  - 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: 62.0%
    - Total number of restraints: 118
    - Weight of restraints: 1.0 (118)
    - Potential type of restraints: square-well-parabolic (118)
    - Range of distance target values: 1.9, 2.75 (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: 121, Sequence coverage: 87.6%
- Total number of restraints: 190
- Total number of restraints per polymer type: 190
- Weight of restraints: 1.0 (190)
- Potential type of restraints: square-well-parabolic (190)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords CenH3 variants, Partially unfolded, centromere protein

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Found 1 Document (0.591 seconds)

BMRB: 18713

Sample #1

Sample #2

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Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. sC4, : 1 entities Detail

Experiments performed 13 experiments Detail

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NMR combined restraints 6 contents Detail