BMRBj - BMREntryMaster

Found 1 Document (0.878 seconds)

BMRB: 25693

2N54

Solution structure of a disulfide stabilized XCL1 dimer

Authors

Tyler, R.C., Tuinstra, R.L., Peterson, F.F., Volkman, B.F.

Assembly

xcL1

Entity

1. xcL1 (polymer, Thiol state: all disulfide bound), 93 monomers, 10335.79 × 2 Da Detail

VGSEVSDKRT CVSLTTQRLP VSRIKTYTIT EGSLRCVIFI TKRGLKVCCD PQATWVRDVV RSMDRKSNTR NNMIQTKPTG TQQSTNTAVT LTG

Total weight

20671.58 Da

Max. entity weight

10335.79 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 74.2 %, Completeness: 64.2 %, Completeness (bb): 67.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	64.2 % (677 of 1055)	62.6 % (343 of 548)	65.8 % (268 of 407)	66.0 % (66 of 100)
Backbone	67.6 % (373 of 552)	68.1 % (128 of 188)	66.1 % (181 of 274)	71.1 % (64 of 90)
Sidechain	62.3 % (368 of 591)	59.7 % (215 of 360)	68.3 % (151 of 221)	20.0 % (2 of 10)
Aromatic	80.0 % (24 of 30)	93.3 % (14 of 15)	64.3 % (9 of 14)	100.0 % (1 of 1)
Methyl	56.9 % (66 of 116)	55.2 % (32 of 58)	58.6 % (34 of 58)

1. XCL1

VGSEVSDKRT CVSLTTQRLP VSRIKTYTIT EGSLRCVIFI TKRGLKVCCD PQATWVRDVV RSMDRKSNTR NNMIQTKPTG TQQSTNTAVT LTG

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.0

#	Name	Isotope labeling	Concentration
1	XCL1	[U-99% 13C; U-99% 15N]	1 mM
2	potassium phosphate	natural abundance	20 mM
3	sodium azide	[U-100% 15N]	0.02 %
4	H2O	natural abundance	90 %
5	D2O	natural abundance	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: -0.65 ppm, Outliers: 1 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: -0.65 ppm, Outliers: 1 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: -0.25 ppm, Outliers: 1 Detail

LACS Plot; CO

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: 1.06 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2N54, Strand ID: A, B Detail

Release date

2015-10-04

Citation

Engineering Metamorphic Chemokine Lymphotactin/XCL1 into the GAG-Binding, HIV-Inhibitory Dimer Conformation
Fox, J.C., Tyler, R.C., Guzzo, C., Tuinstra, R.L., Peterson, F.C., Lusso, P., Volkman, B.F.
ACS Chem. Biol. (2015), 10, 2580-2588, PubMed 26302421 , DOI 10.1021/acschembio.5b00542 , Abstract

Related entities 1. xcL1, : 1 : 7 : 12 entities Detail

Interaction partners 1. xcL1, : 18 interactors Detail

More details for 18 interactors identified by 3 citations

Experiments performed 4 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25693_2n54.nef
Input source #2: Coordindates	2n54.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:11:CYS:SG	A:48:CYS:SG	oxidized, CA 55.61, CB 44.241 ppm	oxidized, CA 55.181, CB 48.662 ppm	2.027
A:36:CYS:SG	A:49:CYS:SG	oxidized, CA 55.839, CB 50.065 ppm	oxidized, CA 56.214, CB 48.015 ppm	2.04
B:211:CYS:SG	B:248:CYS:SG	unknown	unknown	2.022
B:236:CYS:SG	B:249:CYS:SG	unknown	unknown	2.041

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---
VGSEVSDKRTCVSLTTQRLPVSRIKTYTITEGSLRCVIFITKRGLKVCCDPQATWVRDVVRSMDRKSNTRNNMIQTKPTGTQQSTNTAVTLTG
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
VGSEVSDKRTCVSLTTQRLPVSRIKTYTITEGSLRCVIFITKRGLKVCCDPQATWVRDVVRSMDRKSNTRNNMIQTKPTGTQQSTNTAVTLTG

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

-------210-------220-------230-------240-------250-------260-------270-------280-------290---
VGSEVSDKRTCVSLTTQRLPVSRIKTYTITEGSLRCVIFITKRGLKVCCDPQATWVRDVVRSMDRKSNTRNNMIQTKPTGTQQSTNTAVTLTG
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
VGSEVSDKRTCVSLTTQRLPVSRIKTYTITEGSLRCVIFITKRGLKVCCDPQATWVRDVVRSMDRKSNTRNNMIQTKPTGTQQSTNTAVTLTG
--------10--------20--------30--------40--------50--------60--------70--------80--------90---

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	93	0	0	100.0
B	B	93	0	0	100.0

Content subtype: combined_25693_2n54.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	656		71.0 (chain: A, length: 93)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	2084 (1)	noe	60.2 (chain: A, length: 93), 60.2 (chain: B, length: 93)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	108 (108)	.	43.0 (chain: A, length: 93), 43.0 (chain: B, length: 93)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 93, Sequence coverage: 71.0%
- Total number of assignments
  - ¹H chemical shifts: 337
  - ¹³C chemical shifts: 257
  - ¹⁵N chemical shifts: 62
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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	548	337	61.5
¹³C chemical shifts	407	257	63.1
¹⁵N chemical shifts	109	62	56.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	188	124	66.0
¹³C chemical shifts	186	111	59.7
¹⁵N chemical shifts	90	61	67.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	360	213	59.2
¹³C chemical shifts	221	146	66.1
¹⁵N chemical shifts	19	1	5.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	60	30	50.0
¹³C chemical shifts	60	32	53.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	15	14	93.3
¹³C chemical shifts	14	9	64.3
¹⁵N chemical shifts	1	1	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 93, Sequence coverage: 60.2%
  - Entity_assembly_ID: B, Chain length: 93, Sequence coverage: 60.2%
- Total number of restraints: 2065
- Weight of restraints: 1.0 (2065)
- Potential type of restraints: upper-bound-parabolic (2065)
- Range of distance target values: 2.1, 5.5 (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

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 93, Sequence coverage: 43.0%
  - Entity_assembly_ID: B, Chain length: 93, Sequence coverage: 43.0%
- Total number of restraints: 108
- Total number of restraints per polymer type: 108
- Weight of restraints: 1.0 (108)
- Potential type of restraints: square-well-parabolic (108)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue

Keywords ATAC, Chemokine, GAG-binding, HIV-1 inhibition, Lymphotactin, NMR, XCL1, dimer, metamorphic

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.878 seconds)

BMRB: 25693

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. xcL1, : 1 : 7 : 12 entities Detail

Interaction partners 1. xcL1, : 18 interactors Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail