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Found 1 Document (0.943 seconds)

BMRB: 16143

2KED

Structure of SDF-1/CXCL12

Authors

Volkman, B.F., Veldkamp, C.T., Peterson, F.C.

Assembly

CXCL12/SDF1-alpha

Entity

1. CXCL12/SDF1-alpha (polymer, Thiol state: all disulfide bound), 70 monomers, 8151.584 Da Detail

GMKPVSLSYR CPCRFFESHV ARANVKHLKI LNTPNCALQI VARLKNNNRQ VCIDPKLKWI QEYLEKALNK

Formula weight

8151.584 Da

Entity Connection

disulfide 2 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS11:SG	1:CYS36:SG
2	disulfide	sing	1:CYS13:SG	1:CYS52:SG

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.1 %, Completeness: 95.0 %, Completeness (bb): 95.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	95.0 % (829 of 873)	96.5 % (447 of 463)	92.8 % (309 of 333)	94.8 % (73 of 77)
Backbone	95.6 % (394 of 412)	95.6 % (131 of 137)	96.2 % (201 of 209)	93.9 % (62 of 66)
Sidechain	94.9 % (503 of 530)	96.9 % (316 of 326)	91.2 % (176 of 193)	100.0 % (11 of 11)
Aromatic	85.7 % (48 of 56)	100.0 % (28 of 28)	70.4 % (19 of 27)	100.0 % (1 of 1)
Methyl	92.5 % (74 of 80)	100.0 % (40 of 40)	85.0 % (34 of 40)

1. CXCL12/SDF1-alpha

GMKPVSLSYR CPCRFFESHV ARANVKHLKI LNTPNCALQI VARLKNNNRQ VCIDPKLKWI QEYLEKALNK

Show sample condition

Sample

Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 1.6 mM CXCL12 U-15N/13C in 20 mM MES, pH 5.5

#	Name	Isotope labeling	Concentration
1	CXCL12/SDF1-alpha	[U-100% 13C; U-100% 15N]	1.6 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	MES	natural abundance	20 mM

LACS Plot; CA

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

Referencing offset: -0.13 ppm, Outliers: 2 Detail

LACS Plot; CB

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

Referencing offset: -0.13 ppm, Outliers: 2 Detail

LACS Plot; HA

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

Referencing offset: 0.01 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: 0.14 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2009-06-24

Citation

Monomeric structure of the cardioprotective chemokine SDF-1/CXCL12
Veldkamp, C.T., Ziarek, J.J., Su, J., Basnet, H., Lennertz, R., Weiner, J.J., Peterson, F.C., Baker, J.E., Volkman, B.F.
Protein Sci. (2009), 18, 1359-1369, PubMed 19551879 , DOI 10.1002/pro.167 , Abstract

Entries sharing articles BMRB: 2, Swiss-Prot: 1 entries Detail

  BMRB: 16142 released on 2009-06-24
    Title Structure of SDF-1/CXCL12
  BMRB: 16145 released on 2009-06-24
    Title Structure of SDF-1/CXCL12
  Swiss-Prot: P48061 released on 1996-02-01
    Title SDF1_HUMAN Entity Stromal cell-derived factor 1

Related entities 1. CXCL12/SDF1-alpha, : 1 : 1 : 25 : 101 entities Detail

Interaction partners 1. CXCL12/SDF1-alpha, : 27 interactors Detail

More details for 27 interactors identified by 5 citations

Experiments performed 3 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_16143_2ked.nef
Input source #2: Coordindates	2ked.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:9:CYS:SG	A:34:CYS:SG	oxidized, CA 53.127, CB 40.218 ppm	oxidized, CA 54.622, CB 44.78 ppm	2.002
A:11:CYS:SG	A:50:CYS:SG	oxidized, CA 53.429, CB 39.603 ppm	oxidized, CA 56.377, CB 44.694 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

-0--------10--------20--------30--------40--------50--------60--------
GMKPVSLSYRCPCRFFESHVARANVKHLKILNTPNCALQIVARLKNNNRQVCIDPKLKWIQEYLEKALNK
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GMKPVSLSYRCPCRFFESHVARANVKHLKILNTPNCALQIVARLKNNNRQVCIDPKLKWIQEYLEKALNK
--------10--------20--------30--------40--------50--------60--------70

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	70	0	0	100.0

Content subtype: combined_16143_2ked.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_chem_shift_list_1	Warning	826		97.1 (chain: A, length: 70)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	1610 (1)	noe	97.1 (chain: A, length: 70)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	66 (66)	.	74.3 (chain: A, length: 70)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 70, Sequence coverage: 97.1%
- Total number of assignments
  - ¹H chemical shifts: 447
  - ¹³C chemical shifts: 307
  - ¹⁵N chemical shifts: 72
- 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	463	447	96.5
¹³C chemical shifts	333	307	92.2
¹⁵N chemical shifts	82	72	87.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	137	131	95.6
¹³C chemical shifts	140	132	94.3
¹⁵N chemical shifts	66	61	92.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	326	316	96.9
¹³C chemical shifts	193	175	90.7
¹⁵N chemical shifts	16	11	68.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	41	40	97.6
¹³C chemical shifts	41	33	80.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	28	28	100.0
¹³C chemical shifts	27	19	70.4
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: 70, Sequence coverage: 97.1%
- Total number of restraints: 1608
- Weight of restraints: 1.0 (1608)
- Potential type of restraints: upper-bound-parabolic (1608)
- Range of distance target values: 2.0, 5.5 (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: DYANA/DIANA_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 70, Sequence coverage: 74.3%
- Total number of restraints: 66
- Total number of restraints per polymer type: 66
- Weight of restraints: 1.0 (66)
- Potential type of restraints: square-well-parabolic (66)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords chemokine, CXCL12, SDF1-alpha, stromal cell derived factor-1

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Found 1 Document (0.943 seconds)

BMRB: 16143

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 2, Swiss-Prot: 1 entries Detail

Related entities 1. CXCL12/SDF1-alpha, : 1 : 1 : 25 : 101 entities Detail

Interaction partners 1. CXCL12/SDF1-alpha, : 27 interactors Detail

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail