BMRB Entry 16519

Name: Solution structure of human SDF1-alpha H25R
Published: 2012-08-03

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PDB ID: 2kol
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR16519
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution structure of human SDF1-alpha H25R

Deposition date:

2009-09-24

Original release date:

2012-08-03

Authors:

Volkman, B.; Ziarek, J.; Peterson, F.

Citation:

Citation: Ziarek, J.; Veldkamp, C.; Peterson, F.; Volkman, B.. "TBD" To be published ., .-..

Assembly members:

Assembly members:
SDF1a_H25R, polymer, 68 residues, 7997.572 Da.

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pQE30-8HT

Entity Sequences (FASTA):

Entity Sequences (FASTA):
SDF1a_H25R: KPVSLSYRCPCRFFESHVAR ANVKRLKILNTPNCALQIVA RLKNNNRQVCIDPKLKWIQE YLEKALNK

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	319
15N chemical shifts	77
1H chemical shifts	531

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	SDF1a H25R	1

Entities:

Entity 1, SDF1a H25R 68 residues - 7997.572 Da.

1

LYS

PRO

VAL

SER

LEU

SER

TYR

ARG

CYS

PRO

2

CYS

ARG

PHE

GLU

SER

HIS

VAL

ALA

ARG

3

ALA

ASN

VAL

LYS

ARG

LEU

LYS

ILE

LEU

ASN

4

THR

PRO

ASN

CYS

ALA

LEU

GLN

ILE

VAL

ALA

5

ARG

LEU

LYS

ASN

ARG

GLN

VAL

CYS

6

ILE

ASP

PRO

LYS

LEU

LYS

TRP

ILE

GLN

GLU

7

TYR

LEU

GLU

LYS

ALA

LEU

ASN

LYS

Samples:

sample_1: SDF1a H25R, [U-100% 13C; U-100% 15N], 3.3 mM; MES, [U-99% 2H], 25 mM; sodium azide 0.02%; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 20 mM; pH: 6.8; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D_15N-separated_NOESY	sample_1	isotropic	sample_conditions_1
3D_13C-separated_NOESY	sample_1	isotropic	sample_conditions_1
3D_13C-separated_NOESY (AROMATIC)	sample_1	isotropic	sample_conditions_1

Software:

TOPSPIN v2.1, Bruker - collection

NMRPipe v2007, Delagio,F. et al. - processing

XEASY v1.3, Eccles, C., Guntert, P., Billeter, M., Wuthrich, K. - data analysis

SPSCAN v1.1.0, R.W. Glaser - data analysis

GARANT v2.1, C. Bartels - data analysis

CYANA v2.1, Guntert, P. - structural calculation

X-PLOR NIH v2.9.3, SCHWIETERS,C.D.,KUSZEWSKI,J.J.,TJANDRA,N.,CLORE,G.M. - refinement

NMR spectrometers:

Bruker DRX 600 MHz

BMRB	16142 16143 16145
PDB	1A15 1QG7 1SDF 1VMC 2J7Z 2KEC 2KED 2KEE 2KOL 2NWG 2SDF 3HP3 4LMQ 4UAI
DBJ	BAA04648 BAA07862 BAA07863 BAA28601 BAA28602
EMBL	CAG29279 CAH91884 CAJ18596
GB	AAA40100 AAA40101 AAA97434 AAB32650 AAB39332
PIR	I53416
REF	NP_000600 NP_001009847 NP_001012495 NP_001028106 NP_001029058
SP	O62657 P40224 P48061
AlphaFold	O62657 P40224 P48061