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Found 1 Document (0.814 seconds)

BMRB: 17691

2LE4

Solution structure of the HMG box DNA-binding domain of human stem cell transcription factor Sox2

Authors

Sahu, S.C., Markley, J.L., Tonelli, M., Bahrami, A., Eghbalnia, H.R.

Assembly

Sox2

Entity

1. Sox2 (polymer, Thiol state: not present), 81 monomers, 9894.399 Da Detail

SDRVKRPMNA FMVWSRGQRR KMAQENPKMH NSEISKRLGA EWKLLSETEK RPFIDEAKRL RALHMKEHPD YKYRPRRKTK T

Formula weight

9894.399 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 90.6 %, Completeness (bb): 83.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	90.6 % (935 of 1032)	86.3 % (483 of 560)	95.1 % (370 of 389)	98.8 % (82 of 83)
Backbone	83.6 % (398 of 476)	60.4 % (96 of 159)	93.8 % (226 of 241)	100.0 % (76 of 76)
Sidechain	97.0 % (616 of 635)	96.5 % (387 of 401)	98.2 % (223 of 227)	85.7 % (6 of 7)
Aromatic	91.7 % (66 of 72)	97.2 % (35 of 36)	88.2 % (30 of 34)	50.0 % (1 of 2)
Methyl	100.0 % (52 of 52)	100.0 % (26 of 26)	100.0 % (26 of 26)

1. Sox2

SDRVKRPMNA FMVWSRGQRR KMAQENPKMH NSEISKRLGA EWKLLSETEK RPFIDEAKRL RALHMKEHPD YKYRPRRKTK T

Show sample condition

Sample

Solvent system 95% H2O, 5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.7, Details 0.7 mM nanog U-15N/13C, 10 mM MOPS, 5 mM Dithiothreitol, 100 mM NaCl

#	Name	Isotope labeling	Concentration
1	Sox2	[U-100% 13C; U-100% 15N]	0.7 (±0.02) mM
2	DTT	natural abundance	5 (±0.05) %
3	MOPS	natural abundance	10 mM
4	NaCl	natural abundance	100 mM
5	H20	natural abundance	95 %
6	D20	natural abundance	5 %

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: -0.26 ppm, Outliers: 1 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: -0.26 ppm, Outliers: 1 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: 0.16 ppm, Outliers: 1 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: -0.64 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2LE4, Strand ID: A Detail

Release date

2011-07-05

Citation

Not known
Sahu, S., Markley, J., Tonelli, M., Bahrami, A., Eghbalnia, H.
Not known

Related entities 1. Sox2, : 1 : 3 : 17 : 226 entities Detail

Interaction partners 1. Sox2, : 9 interactors Detail

More details for 9 interactors identified by 6 citations

Experiments performed 3 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17691_2le4.nef
Input source #2: Coordindates	2le4.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-
SDRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYRPRRKTKT
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SDRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYRPRRKTKT

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	81	0	0	100.0

Content subtype: combined_17691_2le4.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	sox2Asn	Warning	920		100.0 (chain: A, length: 81)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	1754 (1)	noe	98.8 (chain: A, length: 81)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	60 (1)	hbond	50.6 (chain: A, length: 81)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_4	Warning	361 (354)	.	100.0 (chain: A, length: 81)

Assigned chemical shifts

Saveframe: sox2Asn
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 81, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 470
  - ¹³C chemical shifts: 370
  - ¹⁵N chemical shifts: 80
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- Tautomeric state of HIS
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
68	HIS	HD1	7.963

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	560	469	83.8
¹³C chemical shifts	389	370	95.1
¹⁵N chemical shifts	95	80	84.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	159	81	50.9
¹³C chemical shifts	162	147	90.7
¹⁵N chemical shifts	76	75	98.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	401	388	96.8
¹³C chemical shifts	227	223	98.2
¹⁵N chemical shifts	19	5	26.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	31	31	100.0
¹³C chemical shifts	31	31	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	36	34	94.4
¹³C chemical shifts	34	30	88.2
¹⁵N chemical shifts	2	0	0.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 81, Sequence coverage: 98.8%
- Total number of restraints: 1752
- Weight of restraints: 1.0 (1752)
- Potential type of restraints: upper-bound-parabolic (1752)
- Range of distance target values: 2.4, 10.11 (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: DYANA/DIANA_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 81, Sequence coverage: 50.6%
  - Total number of restraints: 60
  - Weight of restraints: 1.0 (60)
  - Potential type of restraints: upper-bound-parabolic (60)
  - Range of distance target values: 2.0, 3.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_4
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 81, Sequence coverage: 100.0%
- Total number of restraints: 354
- Total number of restraints per polymer type: 354
- Weight of restraints: 1.0 (354)
- Potential type of restraints: square-well-parabolic (354)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Center for Eukaryotic Structural Genomics, Protein Structure Initiative, PSI, Structural Genomics

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Found 1 Document (0.814 seconds)

BMRB: 17691

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Sox2, : 1 : 3 : 17 : 226 entities Detail

Interaction partners 1. Sox2, : 9 interactors Detail

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail