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Found 1 Document (2.758 seconds)

BMRB: 11532

2RTU

solution structure of oxidized human HMGB1 A box

Authors

Jing, W., Tochio, N., Tate, S.

Assembly

oxidized human HMGB1 A box

Entity

1. oxidized human HMGB1 A box (polymer, Thiol state: all disulfide bound), 87 monomers, 10093.45 Da Detail

GSHMGKGDPK KPRGKMSSYA FFVQTCREEH KKKHPDASVN FSEFSKKCSE RWKTMSAKEK GKFEDMAKAD KARYEREMKT YIPPKGE

Formula weight

10093.45 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS26:SG	1:CYS48:SG

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

torsion angle dynamics, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 95.7 %, Completeness (bb): 97.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	95.7 % (1014 of 1060)	93.5 % (534 of 571)	98.5 % (398 of 404)	96.5 % (82 of 85)
Backbone	97.3 % (498 of 512)	97.1 % (170 of 175)	97.6 % (249 of 255)	96.3 % (79 of 82)
Sidechain	94.8 % (596 of 629)	91.9 % (364 of 396)	99.6 % (229 of 230)	100.0 % (3 of 3)
Aromatic	100.0 % (98 of 98)	100.0 % (49 of 49)	100.0 % (48 of 48)	100.0 % (1 of 1)
Methyl	100.0 % (30 of 30)	100.0 % (15 of 15)	100.0 % (15 of 15)

1. entity

GSHMGKGDPK KPRGKMSSYA FFVQTCREEH KKKHPDASVN FSEFSKKCSE RWKTMSAKEK GKFEDMAKAD KARYEREMKT YIPPKGE

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.4

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]	protein	0.5 ~ 0.6 mM
2	potassium phosphate	natural abundance	buffer	50 mM
3	potassium chloride	natural abundance	salt	150 mM
4	D2O	[U-2H]	solvent	10 %
5	H2O		solvent	90 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.844 ppm	internal	indirect	0.2514495
¹H	water	protons	4.844 ppm	internal	direct	1.0
¹⁵N	water	protons	4.844 ppm	internal	indirect	0.1013291

Referencing offset: -0.13 ppm, Outliers: 3 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.844 ppm	internal	indirect	0.2514495
¹H	water	protons	4.844 ppm	internal	direct	1.0
¹⁵N	water	protons	4.844 ppm	internal	indirect	0.1013291

Referencing offset: -0.13 ppm, Outliers: 3 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.844 ppm	internal	indirect	0.2514495
¹H	water	protons	4.844 ppm	internal	direct	1.0
¹⁵N	water	protons	4.844 ppm	internal	indirect	0.1013291

Referencing offset: 0.09 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.844 ppm	internal	indirect	0.2514495
¹H	water	protons	4.844 ppm	internal	direct	1.0
¹⁵N	water	protons	4.844 ppm	internal	indirect	0.1013291

Referencing offset: -0.27 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2014-03-02

Citation

Redox-sensitive structural change in the A-domain of HMGB1 and its implication for the binding to cisplatin modified DNA
Jing, W., Tochio, N., Tate, S.
Biochem. Biophys. Res. Commun. (2013), PubMed 24513216 , DOI 10.1016/j.bbrc.2013.10.085 , Abstract

Related entities 1. oxidized human HMGB1 A box, : 1 : 30 : 292 entities Detail

Interaction partners 1. oxidized human HMGB1 A box, : 59 interactors Detail

More details for 59 interactors identified by 31 citations

Experiments performed 4 experiments Detail

#	Name	Isotope labeling	Type	Concentration
6	entity	[U-13C; U-15N]	protein	0.5 ~ 0.6 mM
7	C12E5/n-hexanol	natural abundance		6 %
8	potassium chloride	natural abundance	salt	150 mM
9	potassium phosphate	natural abundance	buffer	50 mM
10	D2O	[U-2H]	solvent	10 %
11	H2O		solvent	90 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_11532_2rtu.nef
Input source #2: Coordindates	2rtu.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	None
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:26:CYS:SG	A:48:CYS:SG	oxidized, CA 59.131, CB 44.206 ppm	oxidized, CA 58.591, CB 39.928 ppm	2.032

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-------
GSHMGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGE
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSHMGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGE

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	87	0	0	100.0

Content subtype: combined_11532_2rtu.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1017		97.7 (chain: A, length: 87)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	3650 (1)	noe	93.1 (chain: A, length: 87)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	131 (131)	.	86.2 (chain: A, length: 87)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_2	OK	101 (101)	.	60.9 (chain: A, length: 87)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 87, Sequence coverage: 97.7%
- Total number of assignments
  - ¹H chemical shifts: 532
  - ¹³C chemical shifts: 398
  - ¹⁵N chemical shifts: 87
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	571	532	93.2
¹³C chemical shifts	404	398	98.5
¹⁵N chemical shifts	90	87	96.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	175	169	96.6
¹³C chemical shifts	174	169	97.1
¹⁵N chemical shifts	82	79	96.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	396	363	91.7
¹³C chemical shifts	230	229	99.6
¹⁵N chemical shifts	8	8	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	20	20	100.0
¹³C chemical shifts	20	20	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	49	49	100.0
¹³C chemical shifts	48	48	100.0
¹⁵N chemical shifts	1	1	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 87, Sequence coverage: 93.1%
- Total number of restraints: 3532
- Weight of restraints: 1.0 (3532)
- Potential type of restraints: square-well-parabolic (3532)
- Range of distance target values: 2.6, 6.9 (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_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 87, Sequence coverage: 86.2%
- Total number of restraints: 131
- Total number of restraints per polymer type: 131
- Weight of restraints: 1.0 (131)
- Potential type of restraints: square-well-parabolic (131)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 87, Sequence coverage: 60.9%
- Total number of restraints: 101
- Potential type of restraints: undefined (101)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue
  - Chain_ID: A
    None

Keywords disulfide bond, High Mobility Group Box 1

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Found 1 Document (2.758 seconds)

BMRB: 11532

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. oxidized human HMGB1 A box, : 1 : 30 : 292 entities Detail

Interaction partners 1. oxidized human HMGB1 A box, : 59 interactors Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail