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Found 1 Document (2.238 seconds)

BMRB: 30017

5I8N

Solution Structure of human calcium-binding S100A9 (C3S) protein

Authors

Chang, C., Chin, Y.

Assembly

Protein S100-A9

Entity

1. Protein S100-A9 (polymer, Thiol state: not present), 114 monomers, 13225.77 × 2 Da Detail

MTSKMSQLER NIETIINTFH QYSVKLGHPD TLNQGEFKEL VRKDLQNFLK KENKNEKVIE HIMEDLDTNA DKQLSFEEFI MLMARLTWAS HEKMHEGDEG PGHHHKPGLG EGTP

Total weight

26451.54 Da

Max. entity weight

13225.77 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 93.9 %, Completeness: 81.0 %, Completeness (bb): 90.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	81.0 % (1111 of 1372)	78.8 % (570 of 723)	83.5 % (439 of 526)	82.9 % (102 of 123)
Backbone	90.5 % (612 of 676)	86.6 % (201 of 232)	93.1 % (311 of 334)	90.9 % (100 of 110)
Sidechain	74.6 % (598 of 802)	75.2 % (369 of 491)	76.2 % (227 of 298)	15.4 % (2 of 13)
Aromatic	0.0 % (0 of 102)	0.0 % (0 of 51)	0.0 % (0 of 50)	0.0 % (0 of 1)
Methyl	92.0 % (92 of 100)	92.0 % (46 of 50)	92.0 % (46 of 50)

1. entity 1

MTSKMSQLER NIETIINTFH QYSVKLGHPD TLNQGEFKEL VRKDLQNFLK KENKNEKVIE HIMEDLDTNA DKQLSFEEFI MLMARLTWAS HEKMHEGDEG PGHHHKPGLG EGTP

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 (±0.01) atm, Temperature 310 (±0.2) K, pH 7.5 (±0.05), Details 50 mM TRIS, 100 mM sodium chloride, 2 mM calcium chloride, 2 mM [U-13C; U-15N] S100A9 protein (C3S), 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	S100A9 protein (C3S)	[U-13C; U-15N]	2 (±0.2) mM
2	TRIS	natural abundance	50 (±0.2) mM
3	calcium chloride	natural abundance	2 (±0.2) mM
4	sodium chloride	natural abundance	100 (±0.2) mM

LACS Plot; CA

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

Referencing offset: -0.14 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: -0.14 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: 0.05 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: -0.4 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 5I8N, Strand ID: A, B Detail

Release date

2016-08-18

Citation

Blocking the interaction between S100A9 and RAGE V domain using CHAPS molecule: A novel route to drug development against cell proliferation
Chang, C., Khan, I., Tsai, K., Li, H., Yang, L., Chou, R., Yu, C.
Biochim. Biophys. Acta (2016), 1864, 1558-1569, PubMed 27524699 , DOI 10.1016/j.bbapap.2016.08.008 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 26738 released on 2016-09-08
Title 1H, 13C, and 15N Chemical Shift Assignments for Ca2+-bound human mS100A9

Related entities 1. Protein S100-A9, : 1 : 5 : 5 : 54 entities Detail

Interaction partners 1. Protein S100-A9, : 35 interactors Detail

More details for 35 interactors identified by 16 citations

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian VNMRS - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 (±0.01) atm, Temperature 310 (±0.2) K, pH 7.5 (±0.05), Details 50 mM TRIS, 100 mM sodium chloride, 2 mM calcium chloride, 2 mM [U-13C; U-15N] S100A9 protein (C3S), 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	S100A9 protein (C3S)	[U-13C; U-15N]	2 (±0.2) mM
2	TRIS	natural abundance	50 (±0.2) mM
3	calcium chloride	natural abundance	2 (±0.2) mM
4	sodium chloride	natural abundance	100 (±0.2) mM

2 3D HNCA

Instrument

Varian VNMRS - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	S100A9 protein (C3S)	[U-13C; U-15N]	2 (±0.2) mM
2	TRIS	natural abundance	50 (±0.2) mM
3	calcium chloride	natural abundance	2 (±0.2) mM
4	sodium chloride	natural abundance	100 (±0.2) mM

3 3D HN(CO)CA

Instrument

Varian VNMRS - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	S100A9 protein (C3S)	[U-13C; U-15N]	2 (±0.2) mM
2	TRIS	natural abundance	50 (±0.2) mM
3	calcium chloride	natural abundance	2 (±0.2) mM
4	sodium chloride	natural abundance	100 (±0.2) mM

4 3D HNCACB

Instrument

Varian VNMRS - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	S100A9 protein (C3S)	[U-13C; U-15N]	2 (±0.2) mM
2	TRIS	natural abundance	50 (±0.2) mM
3	calcium chloride	natural abundance	2 (±0.2) mM
4	sodium chloride	natural abundance	100 (±0.2) mM

5 3D CBCA(CO)NH

Instrument

Varian VNMRS - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	S100A9 protein (C3S)	[U-13C; U-15N]	2 (±0.2) mM
2	TRIS	natural abundance	50 (±0.2) mM
3	calcium chloride	natural abundance	2 (±0.2) mM
4	sodium chloride	natural abundance	100 (±0.2) mM

6 3D HCCH-TOCSY

Instrument

Varian VNMRS - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	S100A9 protein (C3S)	[U-13C; U-15N]	2 (±0.2) mM
2	TRIS	natural abundance	50 (±0.2) mM
3	calcium chloride	natural abundance	2 (±0.2) mM
4	sodium chloride	natural abundance	100 (±0.2) mM

7 3D H(CCO)NH

Instrument

Varian VNMRS - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	S100A9 protein (C3S)	[U-13C; U-15N]	2 (±0.2) mM
2	TRIS	natural abundance	50 (±0.2) mM
3	calcium chloride	natural abundance	2 (±0.2) mM
4	sodium chloride	natural abundance	100 (±0.2) mM

8 3D C(CO)NH

Instrument

Varian VNMRS - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	S100A9 protein (C3S)	[U-13C; U-15N]	2 (±0.2) mM
2	TRIS	natural abundance	50 (±0.2) mM
3	calcium chloride	natural abundance	2 (±0.2) mM
4	sodium chloride	natural abundance	100 (±0.2) mM

9 3D HN(CA)CO

Instrument

Varian VNMRS - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	S100A9 protein (C3S)	[U-13C; U-15N]	2 (±0.2) mM
2	TRIS	natural abundance	50 (±0.2) mM
3	calcium chloride	natural abundance	2 (±0.2) mM
4	sodium chloride	natural abundance	100 (±0.2) mM

10 3D HNCO

Instrument

Varian VNMRS - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	S100A9 protein (C3S)	[U-13C; U-15N]	2 (±0.2) mM
2	TRIS	natural abundance	50 (±0.2) mM
3	calcium chloride	natural abundance	2 (±0.2) mM
4	sodium chloride	natural abundance	100 (±0.2) mM

11 3D 1H-13C NOESY

Instrument

Varian VNMRS - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	S100A9 protein (C3S)	[U-13C; U-15N]	2 (±0.2) mM
2	TRIS	natural abundance	50 (±0.2) mM
3	calcium chloride	natural abundance	2 (±0.2) mM
4	sodium chloride	natural abundance	100 (±0.2) mM

12 3D 1H-15N NOESY

Instrument

Varian VNMRS - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	S100A9 protein (C3S)	[U-13C; U-15N]	2 (±0.2) mM
2	TRIS	natural abundance	50 (±0.2) mM
3	calcium chloride	natural abundance	2 (±0.2) mM
4	sodium chloride	natural abundance	100 (±0.2) mM

13 3D HBHA(CO)NH

Instrument

Varian VNMRS - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	S100A9 protein (C3S)	[U-13C; U-15N]	2 (±0.2) mM
2	TRIS	natural abundance	50 (±0.2) mM
3	calcium chloride	natural abundance	2 (±0.2) mM
4	sodium chloride	natural abundance	100 (±0.2) mM

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30017_5i8n.nef
Input source #2: Coordindates	5i8n.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
MTSKMSQLERNIETIINTFHQYSVKLGHPDTLNQGEFKELVRKDLQNFLKKENKNEKVIEHIMEDLDTNADKQLSFEEFIMLMARLTWASHEKMHEGDEG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MTSKMSQLERNIETIINTFHQYSVKLGHPDTLNQGEFKELVRKDLQNFLKKENKNEKVIEHIMEDLDTNADKQLSFEEFIMLMARLTWASHEKMHEGDEG

-------110----
PGHHHKPGLGEGTP
||||||||||||||
PGHHHKPGLGEGTP

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

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

-------110----
PGHHHKPGLGEGTP
||||||||||||||
PGHHHKPGLGEGTP

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	114	0	0	100.0
B	B	114	0	0	100.0

Content subtype: combined_30017_5i8n.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1101		93.0 (chain: A, length: 114)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	10582 (1)	noe	92.1 (chain: A, length: 114), 92.1 (chain: B, length: 114)
2	Distance restraints	CNS/XPLOR_distance_constraints_6	OK	3176 (1)	noe	92.1 (chain: A, length: 114), 92.1 (chain: B, length: 114)
3	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	86 (1)	hbond	52.6 (chain: A, length: 114)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	213 (213)	.	97.4 (chain: A, length: 114)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 114, Sequence coverage: 93.0%
- Total number of assignments
  - ¹H chemical shifts: 568
  - ¹³C chemical shifts: 435
  - ¹⁵N chemical shifts: 98
- 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	723	568	78.6
¹³C chemical shifts	526	435	82.7
¹⁵N chemical shifts	126	98	77.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	232	202	87.1
¹³C chemical shifts	228	209	91.7
¹⁵N chemical shifts	110	98	89.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	491	366	74.5
¹³C chemical shifts	298	226	75.8
¹⁵N chemical shifts	16	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	56	50	89.3
¹³C chemical shifts	56	50	89.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	51	0	0.0
¹³C chemical shifts	50	0	0.0
¹⁵N chemical shifts	1	0	0.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 114, Sequence coverage: 92.1%
  - Entity_assembly_ID: B, Chain length: 114, Sequence coverage: 92.1%
- Total number of restraints: 9795
- Weight of restraints: 1.0 (9795)
- Potential type of restraints: square-well-parabolic (9795)
- Range of distance target values: 2.04, 3.0 (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_6
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 114, Sequence coverage: 92.1%
    - Entity_assembly_ID: B, Chain length: 114, Sequence coverage: 92.1%
  - Total number of restraints: 2987
  - Weight of restraints: 1.0 (2987)
  - Potential type of restraints: square-well-parabolic (2987)
  - Range of distance target values: 2.0, 3.0 (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_3
    - Status: OK
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 114, Sequence coverage: 52.6%
    - Total number of restraints: 86
    - Weight of restraints: 1.0 (86)
    - Potential type of restraints: square-well-parabolic (86)
    - Range of distance target values: 2.05, 3.05 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
        None
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 114, Sequence coverage: 97.4%
- Total number of restraints: 213
- Total number of restraints per polymer type: 213
- Weight of restraints: 1.0 (213)
- Potential type of restraints: square-well-parabolic (213)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords METAL BINDING PROTEIN, calcium-binding, calgranulin B, homodimer, migration inhibitory factor-related protein 14 (MRP14)

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Found 1 Document (2.238 seconds)

BMRB: 30017

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. Protein S100-A9, : 1 : 5 : 5 : 54 entities Detail

Interaction partners 1. Protein S100-A9, : 35 interactors Detail

Experiments performed 13 experiments Detail

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NMR combined restraints 6 contents Detail