BMRBj - BMREntryMaster

Found 1 Document (1.072 seconds)

BMRB: 19601

2MGS

Solution structure of CXCL5

Authors

Sepuru, K., Rajarathnam, K.

Assembly

CXCL5

Entity

1. CXCL5 (polymer, Thiol state: all disulfide bound), 78 monomers, 8356.777 × 2 Da Detail

AGPAAAVLRE LRCVCLQTTQ GVHPKMISNL QVFAIGPQCS KVEVVASLKN GKEICLDPEA PFLKKVIQKI LDGGNKEN

Total weight

16713.555 Da

Max. entity weight

8356.777 Da

Entity Connection

disulfide 2 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS13:SG	1:CYS39:SG
2	disulfide	sing	1:CYS15:SG	1:CYS55:SG

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

DGSA-distance geometry simulated annealing, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 50.5 %, Completeness (bb): 74.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	50.5 % (455 of 901)	49.2 % (232 of 472)	44.1 % (153 of 347)	85.4 % (70 of 82)
Backbone	74.5 % (341 of 458)	87.3 % (137 of 157)	58.8 % (134 of 228)	95.9 % (70 of 73)
Sidechain	34.4 % (177 of 515)	30.2 % (95 of 315)	42.9 % (82 of 191)	0.0 % (0 of 9)
Aromatic	0.0 % (0 of 24)	0.0 % (0 of 12)	0.0 % (0 of 12)
Methyl	17.6 % (18 of 102)	15.7 % (8 of 51)	19.6 % (10 of 51)

1. entity

AGPAAAVLRE LRCVCLQTTQ GVHPKMISNL QVFAIGPQCS KVEVVASLKN GKEICLDPEA PFLKKVIQKI LDGGNKEN

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 K, pH 6.0, Details 50 mM sodium phosphate buffer at pH 6.0 containing 0.01% sodium azide and 10 % D2O.

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]	protein	0.4 mM
2	sodium phosphate	natural abundance	buffer	50 mM
3	sodium azide	natural abundance		0.01 %
4	H2O		solvent	90 %
5	D2O		solvent	10 %

LACS Plot; CA

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

Referencing offset: 2.8 ppm, Outliers: 4 Detail

LACS Plot; CB

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

Referencing offset: 2.8 ppm, Outliers: 4 Detail

LACS Plot; HA

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

Referencing offset: -0.41 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2014-03-30

Citation

Solution structure of CXCL5--a novel chemokine and adipokine implicated in inflammation and obesity
Sepuru, K., Poluri, K., Rajarathnam, K.
PLoS One (2014), 9, e93228-e93228, PubMed 24695525 , DOI 10.1371/journal.pone.0093228 , Abstract

Related entities 1. CXCL5, : 1 : 2 : 152 entities Detail

Interaction partners 1. CXCL5, : 7 interactors Detail

More details for 7 interactors identified by 1 citations

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 K, pH 6.0, Details 50 mM sodium phosphate buffer at pH 6.0 containing 0.01% sodium azide and 10 % D2O.

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]	protein	0.4 mM
2	sodium phosphate	natural abundance	buffer	50 mM
3	sodium azide	natural abundance		0.01 %
4	H2O		solvent	90 %
5	D2O		solvent	10 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]	protein	0.4 mM
2	sodium phosphate	natural abundance	buffer	50 mM
3	sodium azide	natural abundance		0.01 %
4	H2O		solvent	90 %
5	D2O		solvent	10 %

3 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]	protein	0.4 mM
2	sodium phosphate	natural abundance	buffer	50 mM
3	sodium azide	natural abundance		0.01 %
4	H2O		solvent	90 %
5	D2O		solvent	10 %

4 3D HNCA

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]	protein	0.4 mM
2	sodium phosphate	natural abundance	buffer	50 mM
3	sodium azide	natural abundance		0.01 %
4	H2O		solvent	90 %
5	D2O		solvent	10 %

5 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]	protein	0.4 mM
2	sodium phosphate	natural abundance	buffer	50 mM
3	sodium azide	natural abundance		0.01 %
4	H2O		solvent	90 %
5	D2O		solvent	10 %

6 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]	protein	0.4 mM
2	sodium phosphate	natural abundance	buffer	50 mM
3	sodium azide	natural abundance		0.01 %
4	H2O		solvent	90 %
5	D2O		solvent	10 %

7 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]	protein	0.4 mM
2	sodium phosphate	natural abundance	buffer	50 mM
3	sodium azide	natural abundance		0.01 %
4	H2O		solvent	90 %
5	D2O		solvent	10 %

8 3D HBHA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]	protein	0.4 mM
2	sodium phosphate	natural abundance	buffer	50 mM
3	sodium azide	natural abundance		0.01 %
4	H2O		solvent	90 %
5	D2O		solvent	10 %

9 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]	protein	0.4 mM
2	sodium phosphate	natural abundance	buffer	50 mM
3	sodium azide	natural abundance		0.01 %
4	H2O		solvent	90 %
5	D2O		solvent	10 %

10 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]	protein	0.4 mM
2	sodium phosphate	natural abundance	buffer	50 mM
3	sodium azide	natural abundance		0.01 %
4	H2O		solvent	90 %
5	D2O		solvent	10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_19601_2mgs.nef
Input source #2: Coordindates	2mgs.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:13:CYS:SG	A:39:CYS:SG	reduced, CA 52.2, CB 29.5 ppm	oxidized, CA 54.3, CB 37.9 ppm	2.033
A:15:CYS:SG	A:55:CYS:SG	reduced, CA 54.3, CB 27.2 ppm	reduced, CB 34.5 ppm	2.037
B:13:CYS:SG	B:39:CYS:SG	unknown	unknown	2.031
B:15:CYS:SG	B:55:CYS:SG	unknown	unknown	2.034

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--------
AGPAAAVLRELRCVCLQTTQGVHPKMISNLQVFAIGPQCSKVEVVASLKNGKEICLDPEAPFLKKVIQKILDGGNKEN
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
AGPAAAVLRELRCVCLQTTQGVHPKMISNLQVFAIGPQCSKVEVVASLKNGKEICLDPEAPFLKKVIQKILDGGNKEN

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

--------10--------20--------30--------40--------50--------60--------70--------
AGPAAAVLRELRCVCLQTTQGVHPKMISNLQVFAIGPQCSKVEVVASLKNGKEICLDPEAPFLKKVIQKILDGGNKEN
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
AGPAAAVLRELRCVCLQTTQGVHPKMISNLQVFAIGPQCSKVEVVASLKNGKEICLDPEAPFLKKVIQKILDGGNKEN

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	78	0	0	100.0
B	B	78	0	0	100.0

Content subtype: combined_19601_2mgs.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	426		100.0 (chain: A, length: 78)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1676 (1)	noe	89.7 (chain: A, length: 78), 89.7 (chain: B, length: 78)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	1426 (1)	noe	59.0 (chain: A, length: 78), 88.5 (chain: B, length: 78)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 78, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 218
  - ¹³C chemical shifts: 138
  - ¹⁵N chemical shifts: 70
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- 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	472	218	46.2
¹³C chemical shifts	347	138	39.8
¹⁵N chemical shifts	84	70	83.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	157	136	86.6
¹³C chemical shifts	156	66	42.3
¹⁵N chemical shifts	73	70	95.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	315	82	26.0
¹³C chemical shifts	191	72	37.7
¹⁵N chemical shifts	11	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	52	6	11.5
¹³C chemical shifts	52	6	11.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	12	0	0.0
¹³C chemical shifts	12	0	0.0

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: 78, Sequence coverage: 89.7%
  - Entity_assembly_ID: B, Chain length: 78, Sequence coverage: 89.7%
- Total number of restraints: 1676
- Weight of restraints: 1.0 (1676)
- Potential type of restraints: square-well-parabolic (1676)
- Range of distance target values: 1.95, 13.75 (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: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 78, Sequence coverage: 59.0%
    - Entity_assembly_ID: B, Chain length: 78, Sequence coverage: 88.5%
  - Total number of restraints: 1426
  - Weight of restraints: 1.0 (1426)
  - Potential type of restraints: square-well-parabolic (1426)
  - Range of distance target values: 1.95, 4.95 (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

Keywords chemokine, CXCR2 activating chemokine, Dimer, ENA78, Neutrophil activating chemokine

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Found 1 Document (1.072 seconds)

BMRB: 19601

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. CXCL5, : 1 : 2 : 152 entities Detail

Interaction partners 1. CXCL5, : 7 interactors Detail

Experiments performed 10 experiments Detail

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NMR combined restraints 4 contents Detail