BMRBj - BMREntryMaster

	Total	¹H	¹³C	¹⁵N
All	88.8 % (938 of 1056)	94.8 % (525 of 554)	78.7 % (322 of 409)	97.8 % (91 of 93)
Backbone	82.6 % (431 of 522)	97.2 % (171 of 176)	68.1 % (179 of 263)	97.6 % (81 of 83)
Sidechain	95.0 % (588 of 619)	93.7 % (354 of 378)	97.0 % (224 of 231)	100.0 % (10 of 10)
Aromatic	100.0 % (40 of 40)	100.0 % (20 of 20)	100.0 % (18 of 18)	100.0 % (2 of 2)
Methyl	100.0 % (118 of 118)	100.0 % (59 of 59)	100.0 % (59 of 59)

1. entity 1

MILEAHYTNL KCRCSGVIST VVGLNIIDRI QVTPPGNGCP KTEVVIWTKM KKVICVNPRA KWLQRLLRHV QSKSLSSTPQ APVSKRRAA

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 850 uM U-[15N] CXCL13, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	CXCL13	[U-15N]	850 uM
2	potassium phosphate	natural abundance	20 mM
3	NaCl	natural abundance	100 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 280 uM U-[13C,15N] CXCL13, 100% D2O

#	Name	Isotope labeling	Concentration
4	CXCL13	[U-13C; U-15N]	280 uM
5	potassium phosphate	natural abundance	20 mM
6	NaCl	natural abundance	100 mM

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 280 uM U-[13C,15N] CXCL13, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
7	CXCL13	[U-13C; U-15N]	280 uM
8	potassium phosphate	natural abundance	20 mM
9	NaCl	natural abundance	100 mM

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 280 uM [U-10% 13C; U-100% 15N] CXCL13, 100% D2O

#	Name	Isotope labeling	Concentration
10	CXCL13	[U-10% 13C; U-100% 15N]	280 uM
11	potassium phosphate	natural abundance	20 mM
12	NaCl	natural abundance	100 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: -0.01 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: -0.01 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: -0.08 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 5IZB, Strand ID: A Detail

Release date

2016-06-09

Citation

Solution structure of CXCL13 and heparan sulfate binding show that GAG binding site and cellular signalling rely on distinct domains
Monneau, Y.R., Luo, L., Sankaranarayanan, N.V., Nagarajan, B., Vives, R.R., Baleux, F., Desai, U.R., Arenzana-Seidedos, F., Lortat-Jacob, H.
Open Biol. (2017), 7, 170133-170133, PubMed 29070611 , DOI 10.1098/rsob.170133 , Abstract

Related entities 1. C-X-C motif chemokine 13, : 1 : 3 : 22 entities Detail

Interaction partners 1. C-X-C motif chemokine 13, : 4 interactors Detail

More details for 4 interactors identified by 2 citations

Experiments performed 18 experiments Detail

1 3D 15N-edited NOESY

Instrument

Bruker AvanceIII - 600 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 850 uM U-[15N] CXCL13, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	CXCL13	[U-15N]	850 uM
2	potassium phosphate	natural abundance	20 mM
3	NaCl	natural abundance	100 mM

2 3D 13C-edited NOESY

Instrument

Bruker AvanceIII - 950 MHz cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 280 uM U-[13C,15N] CXCL13, 100% D2O

#	Name	Isotope labeling	Concentration
4	CXCL13	[U-13C; U-15N]	280 uM
5	potassium phosphate	natural abundance	20 mM
6	NaCl	natural abundance	100 mM

3 3D 13C-HMQC-NOESY-13C,1H-HMQC

Instrument

Bruker AvanceIII - 950 MHz cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 280 uM U-[13C,15N] CXCL13, 100% D2O

#	Name	Isotope labeling	Concentration
4	CXCL13	[U-13C; U-15N]	280 uM
5	potassium phosphate	natural abundance	20 mM
6	NaCl	natural abundance	100 mM

4 3D HNCACB

Instrument

Bruker AvanceIII - 850 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 280 uM U-[13C,15N] CXCL13, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
7	CXCL13	[U-13C; U-15N]	280 uM
8	potassium phosphate	natural abundance	20 mM
9	NaCl	natural abundance	100 mM

5 3D HNCA

Instrument

Bruker AvanceIII - 850 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 280 uM U-[13C,15N] CXCL13, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
7	CXCL13	[U-13C; U-15N]	280 uM
8	potassium phosphate	natural abundance	20 mM
9	NaCl	natural abundance	100 mM

6 3D CBCA(CO)NH

Instrument

Bruker AvanceIII - 850 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 280 uM U-[13C,15N] CXCL13, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
7	CXCL13	[U-13C; U-15N]	280 uM
8	potassium phosphate	natural abundance	20 mM
9	NaCl	natural abundance	100 mM

7 3D HNCO

Instrument

Bruker AvanceIII - 850 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 280 uM U-[13C,15N] CXCL13, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
7	CXCL13	[U-13C; U-15N]	280 uM
8	potassium phosphate	natural abundance	20 mM
9	NaCl	natural abundance	100 mM

8 3D HACACO

Instrument

Bruker AvanceIII - 850 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 280 uM U-[13C,15N] CXCL13, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
7	CXCL13	[U-13C; U-15N]	280 uM
8	potassium phosphate	natural abundance	20 mM
9	NaCl	natural abundance	100 mM

9 3D H(C)CH-TOCSY

Instrument

Bruker AvanceIII - 850 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 280 uM U-[13C,15N] CXCL13, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
7	CXCL13	[U-13C; U-15N]	280 uM
8	potassium phosphate	natural abundance	20 mM
9	NaCl	natural abundance	100 mM

10 3D (H)CCH-TOCSY

Instrument

Bruker AvanceIII - 850 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 280 uM U-[13C,15N] CXCL13, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
7	CXCL13	[U-13C; U-15N]	280 uM
8	potassium phosphate	natural abundance	20 mM
9	NaCl	natural abundance	100 mM

11 2D 1H-13C HSQC aliphatic

Instrument

Bruker AvanceIII - 700 MHz cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 280 uM U-[13C,15N] CXCL13, 100% D2O

#	Name	Isotope labeling	Concentration
4	CXCL13	[U-13C; U-15N]	280 uM
5	potassium phosphate	natural abundance	20 mM
6	NaCl	natural abundance	100 mM

12 2D 1H-13C HSQC aromatic

Instrument

Bruker AvanceIII - 700 MHz cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 280 uM U-[13C,15N] CXCL13, 100% D2O

#	Name	Isotope labeling	Concentration
4	CXCL13	[U-13C; U-15N]	280 uM
5	potassium phosphate	natural abundance	20 mM
6	NaCl	natural abundance	100 mM

13 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 850 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 280 uM U-[13C,15N] CXCL13, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
7	CXCL13	[U-13C; U-15N]	280 uM
8	potassium phosphate	natural abundance	20 mM
9	NaCl	natural abundance	100 mM

14 2D 1H-13C CT-HSQC aliphatic

Instrument

Bruker AvanceIII - 600 MHz cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 280 uM [U-10% 13C; U-100% 15N] CXCL13, 100% D2O

#	Name	Isotope labeling	Concentration
10	CXCL13	[U-10% 13C; U-100% 15N]	280 uM
11	potassium phosphate	natural abundance	20 mM
12	NaCl	natural abundance	100 mM

15 2D COSYdqf

Instrument

Bruker AvanceIII - 700 MHz cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 280 uM [U-10% 13C; U-100% 15N] CXCL13, 100% D2O

#	Name	Isotope labeling	Concentration
10	CXCL13	[U-10% 13C; U-100% 15N]	280 uM
11	potassium phosphate	natural abundance	20 mM
12	NaCl	natural abundance	100 mM

16 2D TOCSY

Instrument

Bruker AvanceIII - 700 MHz cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 280 uM [U-10% 13C; U-100% 15N] CXCL13, 100% D2O

#	Name	Isotope labeling	Concentration
10	CXCL13	[U-10% 13C; U-100% 15N]	280 uM
11	potassium phosphate	natural abundance	20 mM
12	NaCl	natural abundance	100 mM

17 2D CBCGCDHD

Instrument

Bruker AvanceIII - 850 MHz cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 280 uM U-[13C,15N] CXCL13, 100% D2O

#	Name	Isotope labeling	Concentration
4	CXCL13	[U-13C; U-15N]	280 uM
5	potassium phosphate	natural abundance	20 mM
6	NaCl	natural abundance	100 mM

18 3D HNCOCA

Instrument

Bruker AvanceIII - 850 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 280 uM U-[13C,15N] CXCL13, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
7	CXCL13	[U-13C; U-15N]	280 uM
8	potassium phosphate	natural abundance	20 mM
9	NaCl	natural abundance	100 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30042_5izb.nef
Input source #2: Coordindates	5izb.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:12:CYS:SG	A:39:CYS:SG	oxidized, CA 54.556, CB 38.2 ppm	oxidized, CA 52.428, CB 41.847 ppm	2.039
A:14:CYS:SG	A:55:CYS:SG	oxidized, CA 54.58, CB 42.811 ppm	oxidized, CA 57.382, CB 47.876 ppm	2.027

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---------
MILEAHYTNLKCRCSGVISTVVGLNIIDRIQVTPPGNGCPKTEVVIWTKMKKVICVNPRAKWLQRLLRHVQSKSLSSTPQAPVSKRRAA
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MILEAHYTNLKCRCSGVISTVVGLNIIDRIQVTPPGNGCPKTEVVIWTKMKKVICVNPRAKWLQRLLRHVQSKSLSSTPQAPVSKRRAA

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	89	0	0	100.0

Content subtype: combined_30042_5izb.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	929		100.0 (chain: A, length: 89)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1430 (1)	noe	85.4 (chain: A, length: 89)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	38 (1)	hbond	30.3 (chain: A, length: 89)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	110 (110)	.	73.0 (chain: A, length: 89)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 89, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 529
  - ¹³C chemical shifts: 309
  - ¹⁵N chemical shifts: 91
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
48	THR	HG1	5.893

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	554	524	94.6
¹³C chemical shifts	409	309	75.6
¹⁵N chemical shifts	100	91	91.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	176	171	97.2
¹³C chemical shifts	178	85	47.8
¹⁵N chemical shifts	83	81	97.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	378	353	93.4
¹³C chemical shifts	231	224	97.0
¹⁵N chemical shifts	17	10	58.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	61	61	100.0
¹³C chemical shifts	61	61	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	20	20	100.0
¹³C chemical shifts	18	18	100.0
¹⁵N chemical shifts	2	2	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 89, Sequence coverage: 85.4%
- Total number of restraints: 1430
- Weight of restraints: 1.0 (1430)
- Potential type of restraints: square-well-parabolic (1430)
- Range of distance target values: 2.15, 5.04 (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: 89, Sequence coverage: 30.3%
  - Total number of restraints: 38
  - Weight of restraints: 1.0 (38)
  - Potential type of restraints: square-well-parabolic (38)
  - Range of distance target values: 1.98, 2.85 (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: 89, Sequence coverage: 73.0%
- Total number of restraints: 110
- Total number of restraints per polymer type: 110
- Weight of restraints: 1.0 (110)
- Potential type of restraints: square-well-parabolic (110)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Chemokine structure N-terminal domain conformational exchange, Signaling protein

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Found 1 Document (0.615 seconds)

BMRB: 30042

Sample #1

Sample #2

Sample #3

Sample #4

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. C-X-C motif chemokine 13, : 1 : 3 : 22 entities Detail

Interaction partners 1. C-X-C motif chemokine 13, : 4 interactors Detail

Experiments performed 18 experiments Detail

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NMR combined restraints 5 contents Detail